Nutritional metabonomics: applications and perspectives

The future backbone of nutritional science: integrating public health priorities with system-oriented precision nutrition

Adopting policies that promote health for the entire biosphere (One Health) requires human societies to transition towards a more sustainable food supply as well as to deepen the understanding of the metabolic and health effects of evolving food habits. At the same time, life sciences are experiencing rapid and groundbreaking technological developments, in particular in laboratory analytics and biocomputing, placing nutrition research in an unprecedented position to produce knowledge that can be translated into practice in line with One Health policies. In this dynamic context, nutrition research needs to be strategically organised to respond to these societal expectations. One key element of this strategy is to integrate precision nutrition into epidemiological research. This position article therefore reviews the recent developments in nutrition research and proposes how they could be integrated into cohort studies, with a focus on the Swiss research landscape specifically.

Dietary type (carnivore, herbivore and omnivore) and animal species modulate the nutritional metabolome of terrestrial species

Ecometabolomics could be implemented as a powerful tool in molecular ecology studies, but it is necessary to know the baseline of certain metabolites and understand how different traits could affect the metabolome of the animals. Therefore, the main objective of this study was to provide values for the nutritional metabolome profile of different diet groups and animal species, as well as to study the differences in the metabolomic profile due to the effect of diet type and species. To achieve this goal, blood samples were taken from healthy animals (n = 43) of different species: lion (Panthera leo), jaguar (Panthera onca), chimpanzee (Pan troglodytes), bison (Bison bison), gazelle (Gazella cuvieri) and fallow deer (Dama dama), and with different types of diet (carnivore, herbivore and omnivore). Each blood sample was analysed to determine nutritional metabolites. The main results this study provides are the nutritional metabolic profile of these animals based on the type of diet and the animal species. A significant effect of the dietary type was found on nutritional metabolite levels, with those metabolites related to protein metabolism (total protein and creatine) being higher in carnivores. There is also an effect of the species on nutritional metabolites, observing a metabolome differentiation between lion and jaguar. In the case of herbivores, bison showed higher levels of uric acid and cholesterol, and lower urea levels than gazelle and fallow deer. More molecular ecology studies are needed to further the knowledge of the metabolism of these animals.

The application of omics technologies for understanding tropical plants-based bioactive compounds in ruminants: a review

Finding out how diet impacts health and metabolism while concentrating on the functional qualities and bioactive components of food is the crucial scientific objective of nutritional research. The complex relationship between metabolism and nutrition could be investigated with cutting-edge "omics" and bioinformatics techniques. This review paper provides an overview of the use of omics technologies in nutritional research, with a particular emphasis on the new applications of transcriptomics, proteomics, metabolomics, and genomes in functional and biological activity research on ruminant livestock and products in the tropical regions. A wealth of knowledge has been uncovered regarding the regulation and use of numerous physiological and pathological processes by gene, mRNA, protein, and metabolite expressions under various physiological situations and guidelines. In particular, the components of meat and milk were assessed using omics research utilizing the various methods of transcriptomics, proteomics, metabolomics, and genomes. The goal of this review is to use omics technologies-which have been steadily gaining popularity as technological tools-to develop new nutritional, genetic, and leadership strategies to improve animal products and their quality control. We also present an overview of the new applications of omics technologies in cattle production and employ nutriomics and foodomics technologies to investigate the microbes in the rumen ecology. Thus, the application of state-of-the-art omics technology may aid in our understanding of how species and/or breeds adapt, and the sustainability of tropical animal production, in the long run, is becoming increasingly important as a means of mitigating the consequences of climate change.

Enhancing Metabolism and Milk Production Performance in Periparturient Dairy Cattle through Rumen-Protected Methionine and Choline Supplementation

For dairy cattle to perform well throughout and following lactations, precise dietary control during the periparturient phase is crucial. The primary issues experienced by periparturient dairy cows include issues like decreased dry matter intake (DMI), a negative energy balance, higher levels of non-esterified fatty acids (NEFA), and the ensuing inferior milk output. Dairy cattle have always been fed a diet high in crude protein (CP) to produce the most milk possible. Despite the vital function that dairy cows play in the conversion of dietary CP into milk, a sizeable percentage of nitrogen is inevitably expelled, which raises serious environmental concerns. To reduce nitrogen emissions and their production, lactating dairy cows must receive less CP supplementation. Supplementing dairy cattle with rumen-protected methionine (RPM) and choline (RPC) has proven to be a successful method for improving their ability to use nitrogen, regulate their metabolism, and produce milk. The detrimental effects of low dietary protein consumption on the milk yield, protein yield, and dry matter intake may be mitigated by these nutritional treatments. In metabolic activities like the synthesis of sulfur-containing amino acids and methylation reactions, RPM and RPC are crucial players. Methionine, a limiting amino acid, affects the production of milk protein and the success of lactation in general. According to the existing data in the literature, methionine supplementation has a favorable impact on the pathways that produce milk. Similarly, choline is essential for DNA methylation, cell membrane stability, and lipid metabolism. Furthermore, RPC supplementation during the transition phase improves dry matter intake, postpartum milk yield, and fat-corrected milk (FCM) production. This review provides comprehensive insights into the roles of RPM and RPC in optimizing nitrogen utilization, metabolism, and enhancing milk production performance in periparturient dairy cattle, offering valuable strategies for sustainable dairy farming practices.

Foodomics-Based Approaches Shed Light on the Potential Protective Effects of Polyphenols in Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) is a chronic and progressive inflammatory disorder affecting the gastrointestinal tract (GT) caused by a wide range of genetic, microbial, and environmental factors. IBD is characterized by chronic inflammation and decreased gut microbial diversity, dysbiosis, with a lower number of beneficial bacteria and a concomitant increase in pathogenic species. It is well known that dysbiosis is closely related to the induction of inflammation and oxidative stress, the latter caused by an imbalance between reactive oxygen species (ROS) production and cellular antioxidant capacity, leading to cellular ROS accumulation. ROS are responsible for intestinal epithelium oxidative damage and the increased intestinal permeability found in IBD patients, and their reduction could represent a potential therapeutic strategy to limit IBD progression and alleviate its symptoms. Recent evidence has highlighted that dietary polyphenols, the natural antioxidants, can maintain redox equilibrium in the GT, preventing gut dysbiosis, intestinal epithelium damage, and radical inflammatory responses. Here, we suggest that the relatively new foodomics approaches, together with new technologies for promoting the antioxidative properties of dietary polyphenols, including novel delivery systems, chemical modifications, and combination strategies, may provide critical insights to determine the clinical value of polyphenols for IBD therapy and a comprehensive perspective for implementing natural antioxidants as potential IBD candidate treatment.

New Approach for the Identification of Isobaric and Isomeric Metabolites

The structural elucidation of metabolite molecules is important in many branches of the life sciences. However, the isomeric and isobaric complexity of metabolites makes their identification extremely challenging, and analytical standards are often required to confirm the presence of a particular compound in a sample. We present here an approach to overcome these challenges using high-resolution ion mobility spectrometry in combination with cryogenic vibrational spectroscopy for the rapid separation and identification of metabolite isomers and isobars. Ion mobility can separate isomeric metabolites in tens of milliseconds, and cryogenic IR spectroscopy provides highly structured IR fingerprints for unambiguous molecular identification. Moreover, our approach allows one to identify metabolite isomers automatically by comparing their IR fingerprints with those previously recorded in a database, obviating the need for a recurrent introduction of analytical standards. We demonstrate the principle of this approach by constructing a database composed of IR fingerprints of eight isomeric/isobaric metabolites and use it for the identification of these isomers present in mixtures. Moreover, we show how our fast IR fingerprinting technology allows to probe the IR fingerprints of molecules within just a few seconds as they elute from an LC column. This approach has the potential to greatly improve metabolomics workflows in terms of accuracy, speed, and cost.

Almond Consumption for 8 Weeks Altered Host and Microbial Metabolism in Comparison to a Control Snack in Young Adults

Almond consumption can improve cardiometabolic (CM) health. However, the mechanisms underlying those benefits are not well characterized. This study explored the effects of consuming a snack of almonds vs. crackers for 8 weeks on changes in metabolomic profiles in young adults (clinicaltrials.gov ID: NCT03084003).

Participants (n = 73, age: 18-19 years, BMI: 18-41 kg/m2) were randomly assigned to consume either almonds (2 oz/d, n = 38) or an isocaloric control snack of graham crackers (325 kcal/d, n = 35) daily for 8 weeks. Blood samples were collected at baseline prior to and at 4 and 8 weeks after the intervention. Metabolite abundances in the serum were quantified by hydrophilic interaction chromatography quadrupole (Q) time-of-flight (TOF) mass spectrometry (MS/MS), gas chromatography (GC) TOF MS, CSH-ESI (electrospray) QTOF MS/MS, and targeted analyses for free PUFAs, total fatty acids, oxylipins and endocannabinoids. Linear mixed model analyses with baseline-adjustment were conducted, and those results were used for enrichment and network analyses. Microbial community pathway predictions from 16S rRNA sequencing of fecal samples was done using PICRUST2.

Almond consumption enriched unsaturated triglycerides, unsaturated phosphatidylcholines, saturated and unsaturated lysophosphatidylcholines, tricarboxylic acids, and tocopherol clusters (p < 0.05). Targeted analyses reveal lower levels of omega-3 total fatty acids (TFAs) overall in the almond group compared to the cracker group (p < 0.05). Microbial amino acid biosynthesis, and amino sugar and nucleotide sugar metabolism pathways were also differentially enriched at the end of the intervention (p < 0.05).

The study demonstrates the differential effects of almonds on host tocopherol, lipid, and TCA cycle metabolism with potential changes in microbial metabolism, which may interact with host metabolism to facilitate the CM benefits.

Current challenges and future implications of exploiting the omics data into nutrigenetics and nutrigenomics for personalized diagnosis and nutrition-based care

Nutrigenetics and nutrigenomics, combined with the omics technologies, are a demanding and an increasingly important field in personalizing nutrition-based care to understand an individual's response to nutrition-guided therapy. Omics is defined as the analysis of the large data sets of the biological system featuring transcriptomics, proteomics, and metabolomics and providing new insights into cell regulation. The effect of combining nutrigenetics and nutrigenomics with omics will give insight into molecular analysis, as human nutrition requirements vary per individual. Omics measures modest intraindividual variability and is critical to exploit these data for use in the development of precision nutrition. Omics, combined with nutrigenetics and nutrigenomics, is instrumental in the creation of goals for improving the accuracy of nutrition evaluations. Although dietary-based therapies are provided for various clinical conditions such as inborn errors of metabolism, limited advancement has been done to expand the omics data for a more mechanistic understanding of cellular networks dependent on nutrition-based expression and overall regulation of genes. The greatest challenge remains in the clinical sector to integrate the current data available, overcome the well-established limits of self-reported methods in research, and provide omics data, combined with nutrigenetics and nutrigenomics research, for each individual. Hence, the future seems promising if a design for personalized, nutrition-based diagnosis and care can be implemented practically in the health care sector.

Unravelling the Role of Metabolites for Detecting Physiological State of Wild Animals: European Rabbit's (Oryctolagus cuniculus) Case

European wild rabbit (Oryctolagus cuniculus) has been defined as a keystone species in the Mediterranean ecosystem. Rabbits have been classed as "endangered" by the IUCN within their native range. In this sense, animal nutrition may play a fundamental and limiting role in the conservation of wild species. The overarching goal of ecological nutrition is to unravel the extensive web of nutritional links that direct animals in their interactions with their ecological environments. The main aim of this work was to evaluate the effect of different feed intake, geographic location, animal sex, and reproductive stage on glucose, non-esterified fatty acids (NEFA), and plasmatic urea nitrogen (PUN), albumin, glutamate, and total protein metabolites. Additionally, we examined the potential of these metabolites as biomarkers. Full stomach contents and blood samples were collected from European wild rabbits (n = 89) for the analysis of the metabolites described above. Our work shows that the levels of these metabolites are affected by the sex of the animals, as well as by their reproductive stage (glucose, NEFA and albumin). There were signs of better optimisation of resources by females than by other groups of animals. These data may be interesting in the study of nutritional components that could be affecting physiological state of this species.

Nutritional Metabolites as Biomarkers of Previous Feed Intake in European Rabbit (Oryctolagus cuniculus): Applications on Conservation

European wild rabbit (Oryctolagus cuniculus) populations have drastically reduced, and recently, rabbits have been classed as “endangered” by the IUCN. This animal plays an important ecological role in Mediterranean ecosystems and its introduction could significantly contribute to ecological restoration. Rabbits have high nutrient requirements that apparently cannot be covered in all ecosystems, and there are clues that nutrition can limit their abundance and density. On the other hand, some studies reflect the effects of food availability on the metabolomic status of other animal species, but there are no specific studies on this keystone species. The main aim of this work is to find biomarkers to assess the previous levels of ingestion of European rabbits (Oryctolagus cuniculus). To address this gap, gastric content and blood samples were collected from European rabbits (n = 99) in a Mediterranean area for the analysis of glucose, non-esterified fatty acids (NEFA), plasmatic urea nitrogen (PUN), albumin, glutamate and total protein metabolites. Depending on their previous feed intake (gastric content and the ratio between the gastric content and the weight of the animal), the animals were divided into two groups (lower and normal previous feed intake). Our work shows that the metabolomic profiles of the animals were affected. Levels of glucose (+82%; p = 0.0003), NEFA (−61%; p = 0.0040) and PUN (+139%; p < 0.001) were different in the animals with lower previous feed intake than the animals with normal previous feed intake. This work summarises that metabolic phenotype can be interesting when seeking to discover the limiting nutrients and food availability in diets that could affect the ecological fitness and conservation of European wild rabbits. It is important to mention that in this work, only the effects on six different metabolites have been analysed and more studies are necessary to complement the knowledge of possible metabolites that indicate the level of ingestion in this species and others. These (and new) biomarkers could be used as a tool to provide information about individual or population characteristics that other physiological parameters cannot detect, improving the conservation physiology field.

Effect of Supplementation with Olive Leaf Extract Enriched with Oleuropein on the Metabolome and Redox Status of Athletes’ Blood and Urine—A Metabolomic Approach

Oleuropein (OE) is a secoiridoid glycoside occurring mostly in the Oleaceae family and presenting several pharmacological properties, including hypolipidemic and antioxidant properties. Based on these, several dietary supplements containing olive leaf extracts enriched with OE are commercially available in many countries. The current study aimed to examine the effect of supplementation with such an extract on the serum and urine metabolome of young healthy male athletes. For this purpose, applying a randomized, balanced, double-blind study, nine young, healthy males (physical education students) received either a commercially prepared extract or placebo for one week, followed by a two-week washout period; then, they were subsequently dosed with the alternate scheme (crossover design). Urine and serum samples were analyzed using UHPLC-HRMS, followed by evaluation with several multivariate methods of data analysis. The data were interpreted using a multilevel metabolomic approach (multilevel-sPLSDA) as it was found to be the most efficient approach for the study design. Metabolic pathway analysis of the most affected metabolites revealed that tryptophan and acylcarnitine’s biochemistries were most influenced. Furthermore, several metabolites connected to indole metabolism were detected, which may indicate enhanced serotonin turnover. Phenylethylamine and related metabolites, as well as estrone, were connected to enhanced performance. In addition, possible changes to the lipidemic profile and the blood and urine redox statuses were investigated.

The Effect of Feeding Restriction on the Microbiota and Metabolome Response in Late-Phase Laying Hens

Simple Summary

Feeding restriction (FR) is essential to reduce excessive fat deposits caused by overfeeding in hens and to ensure their reasonable nutritional requirements for egg production. Effective FR is particularly crucial for raising hens in the late phase of laying; because hens require lower energy at this stage, overfeeding reduces their feed efficiency and increase feed costs. The gut microbiota is involved in various metabolic pathways of laying hens, including in late-phase age. Thus, changes in feeding interventions can alter the presence of gut microorganisms and the structure of the microbial community, resulting in altered metabolic regulation. In this study, we investigate the microbiota and metabolome responses of late-phase laying hens under FR. Our results provide data to access the profile of the cecal bacteria community, their relevance to cecal and serum metabolites, and their FR biosynthetic pathways related to host nutritional requirements and intestinal nutrient availability. Moreover, understanding the principles of host-microbial interaction is essential for developing cost-effective strategies to improve laying hens’ production.

Abstract

This study investigated cecal bacterial community profile, cecal and serum metabolites, and its biosynthesis pathway in late-phase laying hens during 6 weeks feeding restriction (FR), using 16S rDNA as gene sequencing and non-targeted LC-MS/MS as metabolomics approach. We used three groups (ad libitum, FR20, and FR40). FR can reduce excessive fat in late-phase laying hens, while egg production rate is not affected, except for the FR40 group. In phylum level, FR20 had more population of Bacteriodetes and Firmicutes amongst groups. The same result is at genus level, FR20 were higher of the predominant genus (Bacteroides and Rikenellaceae_RC9_gut_group). Both of FR20 and FR40 reduced Proteobacteria as potential pathogenic bacteria. Non-targeted metabolomic analysis revealed that FR20 modified 20 metabolites in cecal and 10 metabolites in serum of laying hens, whereas 48 cecal metabolites and 31 serum metabolites has revealed in FR40. KEGG assay showed FR20 and FR40 upregulated lipid, carbohydrate, amino acid, nucleic acid pathway, and FR40 modified steroid metabolism in cecal analysis. In serum, only FR40 modified lipid, amino acid pathway, and carbohydrate biosynthesis were shown. This study showed that FR during late-phase laying hens altered the microbiome composition, modified metabolites profile and biosynthesis of the cecal as well as serum.

Nuclear Magnetic Resonance-Based Metabolomic Analysis Reveals Physiological Stage, Breed, and Diet Effects on the Intramuscular Metabolism of Amino Acids and Related Nutrients in Pigs

Skeletal muscle is a complex tissue that exhibits considerable plasticity in response to nutrients, animal, or its growth stage, but the underlying mechanisms are largely unknown. This study was conducted to evaluate the effects of physiological stage, breed, and diet on the metabolome of the skeletal muscle of pigs. Ninety-six barrows, including 48 purebred Bama mini-pigs, representing the fat type, and 48 Landrace pigs, representing the lean type, were randomly assigned to either a low- or adequate-protein diet (n = 24 per group). The experimental period commenced at 5 weeks of age and extended to the finishing period. Psoas major muscles (PMMs) were collected at the nursery, growing, and finishing stages; and the contents of amino acids (AAs), fatty acids (FAs), and metabolites were analyzed using a nuclear magnetic resonance-based approach. Results showed that most AAs and monounsaturated FAs (MUFAs; including C16:1 and C18:1) contents were increased (p < 0.05) gradually, while those of polyunsaturated FAs (including C18:2, C20:4n−6, C20:5n−3, and C22:6n−3) were decreased (p < 0.05) in the PMM with increasing age. Compared with Landrace pigs, Bama mini-pigs had higher (p < 0.05) contents of flavor-related AAs (including methionine, phenylalanine, tyrosine, leucine, and serine) in the nursery and growing stages and higher (p < 0.05) percentages of saturated FAs and MUFAs throughout the trial. Dietary protein levels affected the muscular profiles of AAs and FAs in an age-dependent manner. In addition, the adequate-protein diet increased (p < 0.05) the muscular contents of α-ketoglutarate in the two breeds. These findings indicate that the dynamic profiles of AAs, FAs, and metabolites in pig muscle tissues are regulated by breed, diet, and physiological stage.

Omic methodologies for assessing metal(-loid)s-host-microbiota interplay: A review

Omic methodologies have become key analytical tools in a wide number of research topics such as systems biology, environmental analysis, biomedicine or food analysis. They are especially useful when they are combined providing a new perspective and a holistic view of the analytical problem. Methodologies for microbiota analysis have been mostly focused on genome sequencing. However, information provided by these metagenomic studies is limited to the identification of the presence of genes, taxa and their inferred functionality. To achieve a deeper knowledge of microbial functionality in health and disease, especially in dysbiosis conditions related to metal and metalloid exposure, the introduction of additional meta-omic approaches including metabolomics, metallomics, metatranscriptomics and metaproteomics results essential. The possible impact of metals and metalloids on the gut microbiota and their effects on gut-brain axis (GBA) only begin to be figured out. To this end new analytical workflows combining powerful tools are claimed such as high resolution mass spectrometry and heteroatom-tagged proteomics for the absolute quantification of metal-containing biomolecules using the metal as a "tag" in a sensitive and selective detector (e.g. ICP-MS). This review focus on current analytical methodologies related with the analytical techniques and procedures available for metallomics and microbiota analysis with a special attention on their advantages and drawbacks.

Post-Mortem Metabolomics: A Novel Approach in Clinical Biomarker Discovery and a Potential Tool in Death Investigations

Metabolomics can be defined as the scientific field aiming at characterizing all low-weight molecules (so-called metabolites) in a biological system. At the time of death, the level and type of metabolites present will most likely reflect the events leading up to death.In this proof of concept study, we investigated the potential of post-mortem metabolomics by identifying post-mortem biomarkers, correlated these identified biomarkers with those reported in clinical metabolomics studies, and finally validated the models predictability of unknown autopsy cases. In this post-mortem metabolomics setting, ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry data from 404 post-mortem samples, including pneumonia cases and control cases, were processed using XCMS (R). Potential biomarkers were evaluated using principal component analysis and orthogonal partial least squares-discriminant analysis. Biomarkers were putatively annotated using an in-house database and the online databases METLIN and HMDB. The results showed that clear group separation was observed between pneumonia cases and control cases. The metabolites responsible for group separation belonged to a broad set of biological classes, such as amino acids, carnitines, lipids, nicotinamides, nucleotides, and steroids. Many of these metabolites have been reported as important in clinical manifestation of pneumonia. For the unknown autopsy cases, the sensitivity and specificity were 86 and 84%, respectively. This study successfully investigated the robustness and usability of post-mortem metabolomics in death investigations. The identified post-mortem biomarkers correlated well with biomarkers reported and identified through clinical research.

Metabolism response of grazing yak to dietary concentrate supplementation in warm season

Supplementary feeding has a significant effect on the growth performance of grazing yaks. However, as far as is known, little information is available concerning how energy or protein feed supplementation affects the serum metabolome of grazing yaks during the warm season. We investigated the effects of supplementation with two different concentrates on the serum metabolome in grazing yaks using nuclear magnetic resonance spectroscopy in conjunction with multivariate data analysis. Twenty-four 2-year-old female yaks (133.04 ± 6.52 kg BW) were randomly divided into three groups and fed three different regimes (n = 8 per group): (1) grazing plus hull-less barley (HLB) supplementation, (2) grazing plus rapeseed meal (RSM) supplementation, and (3) grazing without supplementation. Both HLB and RSM supplementation significantly increased the average daily gain (ADG), and ADG under HLB supplementation was 11.9% higher (P < 0.05) than that of the RSM group. Supplementation markedly altered glucose, lipid, and protein metabolism, with the difference manifested as increased levels of some amino acids, acetyl-glycoproteins, low-density lipoproteins, and very low-density lipoproteins . Furthermore, the levels of 3-hydroxybutyrate, acetoacetate, and lactate metabolism were decreased. Serum metabolite changes in yaks in the HLB supplementation treatment differed from those in the RSM supplementation treatment; the difference was primarily manifested in lipid- and protein-related metabolites. We conclude that both the energy supplementation (HLB) and the protein supplementation (RSM) could remarkably promote the growth of yak heifers during the warm season, and the effect of energy supplementation was superior. Supplementary feeding changed the serum metabolite levels of yak heifers, indicating that such feeding could improve glucose's energy-supply efficiency and increase the metabolic intensity of lipids and proteins. Supplementation of yaks with HLB was more efficient in the promotion of yak glucose and protein anabolism compared to supplementation with RSM, while having a lesser effect on lipid metabolism.

Amino Acids in Endoplasmic Reticulum Stress and Redox Signaling

Proteins are the chains of amino acids linked via peptide bonds. In cells, newly synthesized proteins are modified and folded in the endoplasmic reticulum (ER) and matured to be functional proteins before they are transported to other tissues or organs. In addition to protein synthesis, the ER is also a stress-sensing organelle for diverse biological functions, such as calcium storage, lipid synthesis, and cellular metabolism. Nutrient deprivation, accumulation of reactive oxygen species, and other intracellular insults can activate ER stress and unfolded protein response (UPR) to restore homeostasis. Dysfunction of the ER influences cellular physiology and metabolism, and contributes to the pathogenesis of various diseases. Amino acids are the building blocks for proteins of eukaryotic organisms. Both in vivo and in vitro studies have found that amino acids can function as signaling molecules to regulate gene expression, cell proliferation and apoptosis, immune response, and antioxidant capacity in numerous biological processes. Importantly, several lines of studies have indicated that amino acids regulate the abundances of proteins implicated in UPR and the redox state, therefore restoring the intracellular homeostasis. Amino acids play an important role in regulating ER stress and redox homeostasis in animal cells for their survival, growth, and development.

Shenling Baizhu San improves functional dyspepsia in rats as revealed by 1H-NMR based metabolomics

Functional dyspepsia (FD), a common gastrointestinal disorder around the world, is driven by multiple factors, making prevention and treatment a major challenge. Shenling Baizhu San (SBS), a classical prescription of traditional Chinese medicine, has been proven to be effective in gastrointestinal disorders. However, studies on SBS improving FD are few. Thus, our study aimed to evaluate the effect of SBS on FD and further to explore the mechanism underlying the interactions between FD and SBS by the metabolomics approach. A FD rat model was induced by multiple forms of mild stimulation, and proton nuclear magnetic resonance (1H-NMR) spectroscopy and multivariate data analysis were used to profile the fecal and urinary metabolome in the FD rats during SBS intervention. Significant dyspeptic symptoms such as weight loss, poor appetite, reduced gastrointestinal motility and decreased absorptive capacity were observed in the FD rats, which were subsequently improved by SBS. Additionally, the levels of citrate, branched chain acids and pyruvate decreased, and the levels of choline, trimethylamine and taurine increased in the FD rats. Furthermore, the metabolic disorders were amended with SBS intervention mainly by modulating the metabolic pathways involved in energy metabolism, amino acid metabolism, and gut microbiota and host co-metabolism. Overall, our study highlighted the effect of SBS on the disturbed metabolic pathways in the FD rats, providing new insight into the mechanism of SBS treatment for FD from the perspective of metabolomics.

Integrative analysis of the gut microbiota and metabolome in rats treated with rice straw biochar by 16S rRNA gene sequencing and LC/MS-based metabolomics

The intestinal microbiota contributes to host metabolism and health. This study aimed to assess the effects of biochar on cecal microbiome-related metabolic changes in rats. Rats were orally administered rice straw biochar (RSB) at 1120 mg/kg body weight for 5 weeks. Cecal samples were analyzed to perform metabolic and microbial profiling via a combination of 16S rRNA gene sequencing and LC/MS techniques. We observed a significant influence of RSB in shaping the cecal bacterial community, including some potentially beneficial members of phylum Firmicutes belonging to unclassified Lachnospiraceae, Oscillibacter, and Clostridium XlVa and IV, as well as the depletion of some opportunistic pathogens belonging to Prevotella, Bacteroides and Paraprevotella. The metabolomic analysis revealed distinct changes in the cecal metabolic phenotype, including lower levels of L-isoleucine, indole-3-acetic acid, benzoic acid, and tetradecanoic acid as well as higher levels of L-phenylalanine, L-glutamate, 3-phenylpropanoic acid, chenodeoxycholic acid, cholic acid, 7-dehydrocholesterol, (5Z, 8Z, 11Z, 14Z, 17Z)-eicosapentaenoic acid, 11-deoxycorticosterone and retinol, which are mainly involved in the metabolic pathways of linoleic acid, amino acid and steroid hormone biosynthesis. Correlation analysis revealed a positive association of unclassified Lachnospiraceae, Oscillibacter and Clostridium IV with 3-phenylpropanoic acid, L-phenylalanine, L-glutamate, 11-deoxycorticosterone and 7-dehydrocholesterol. These results confirm that the gut microbiome is altered and may be critical for good performance under RSB application by interacting with metabolism.

Postoperative serum metabolites of patients on a low carbohydrate ketogenic diet after pancreatectomy for pancreatobiliary cancer: a nontargeted metabolomics pilot study

A ketogenic diet is a potential adjuvant cancer therapy that limits glucose availability to tumours while fuelling normal tissues with ketone bodies. We examined the effect of a low carbohydrate ketogenic diet (LCKD) (80% kcal from fat, ketogenic ratio 1.75:1, w/w) compared to a general hospital diet (GD) on serum metabolic profiles in patients (n = 18, ≥ 19 years old) who underwent pancreatectomy for pancreatobiliary cancer. Serum samples collected preoperatively (week 0) and after the dietary intervention (week 2) were analysed with a nontargeted metabolomics approach using liquid chromatography-tandem mass spectrometry. Serum β-hydroxybutyrate and total ketone levels significantly increased after 2 weeks of LCKD compared to GD (p < 0.05). Principal component analysis score plots and orthogonal partial least squares discriminant analysis also showed significant differences between groups at week 2, with strong validation. In all, 240 metabolites differed between LCKD and GD. Pathways including glycerophospholipid and sphingolipid metabolisms were significantly enriched in the LCKD samples. LCKD decreased C22:1-ceramide levels, which are reported to be high in pancreatic cancer, while increasing lysophosphatidylcholine (18:2), uric acid, citrulline, and inosine levels, which are generally low in pancreatic cancer. Postoperative LCKD might beneficially modulate pancreatic cancer-related metabolites in patients with pancreatobiliary cancer.

Data analysis of MS-based clinical lipidomics studies with crossover design: A tutorial mini-review of statistical methods

Clinical lipidomics using mass spectrometry (MS) is important to support discovery of biomarkers for diagnosis and understanding the pathophysiology of diseases. Frequently, lipidomics data from clinical studies have large variations among individuals because the human metabolome/lipidome is strongly influenced by genotype, daily activity, diet and gut flora. This inter-personal variability makes data analysis more complex and normally requires a large cohort for robust statistical analysis. Crossover designed experiments treat each subject as his or her own control, thereby reducing the between-subject variability, such that the effects of exposure/treatment are more likely to be identified when using a relatively small number of subjects. This design repeatedly samples an individual when crossing over from one treatment/exposure to another during the course of the study. The acquired datasets have a distinct data structure resulting from repeated longitudinal measurements. A variety of statistical methods are used in published crossover studies, but many appear to ignore the data structure inherent in the experimental design. An appropriate data analysis approach is critical to discovering robust clinical biomarkers. Hereby, we summarize the statistical methodologies suitable for clinical lipidomics studies using crossover design. To help understand and apply these methods to practical cases, we focused on the general concepts of statistical models in the context of analysis of metabolomics data without spending too much effort on mathematical details. Importantly, we aim to evaluate these methods and provide suggestions for data analysis and biomarker discovery. We applied the discussed methods on a MS-based lipidomics dataset from a double-blind random crossover designed clinical dietary intervention study. The strength and potential pitfalls of each method are briefly discussed and a suggestion for analytic workflow proposed.

Comparison of Bi- and Tri-Linear PLS Models for Variable Selection in Metabolomic Time-Series Experiments

Metabolomic studies with a time-series design are widely used for discovery and validation of biomarkers. In such studies, changes of metabolic profiles over time under different conditions (e.g., control and intervention) are compared, and metabolites responding differently between the conditions are identified as putative biomarkers. To incorporate time-series information into the variable (biomarker) selection in partial least squares regression (PLS) models, we created PLS models with different combinations of bilinear/trilinear X and group/time response dummy Y. In total, five PLS models were evaluated on two real datasets, and also on simulated datasets with varying characteristics (number of subjects, number of variables, inter-individual variability, intra-individual variability and number of time points). Variables showing specific temporal patterns observed visually and determined statistically were labelled as discriminating variables. Bootstrapped-VIP scores were calculated for variable selection and the variable selection performance of five PLS models were assessed based on their capacity to correctly select the discriminating variables. The results showed that the bilinear PLS model with group × time response as dummy Y provided the highest recall (true positive rate) of 83–95% with high precision, independent of most characteristics of the datasets. Trilinear PLS models tend to select a small number of variables with high precision but relatively high false negative rate (lower power). They are also less affected by the noise compared to bilinear PLS models. In datasets with high inter-individual variability, bilinear PLS models tend to provide higher recall while trilinear models tend to provide higher precision. Overall, we recommend bilinear PLS with group x time response Y for variable selection applications in metabolomics intervention time series studies.

Metabolomics and Microbiomes as Potential Tools to Evaluate the Effects of the Mediterranean Diet

The approach to studying diet–health relationships has progressively shifted from individual dietary components to overall dietary patterns that affect the interaction and balance of low-molecular-weight metabolites (metabolome) and host-enteric microbial ecology (microbiome). Even though the Mediterranean diet (MedDiet) has been recognized as a powerful strategy to improve health, the accurate assessment of exposure to the MedDiet has been a major challenge in epidemiological and clinical studies. Interestingly, while the effects of individual dietary components on the metabolome have been described, studies investigating metabolomic profiles in response to overall dietary patterns (including the MedDiet), although limited, have been gaining attention. Similarly, the beneficial effects of the MedDiet on cardiometabolic outcomes may be mediated through gut microbial changes. Accumulating evidence linking food ingestion and enteric microbiome alterations merits the evaluation of the microbiome-mediated effects of the MedDiet on metabolic pathways implicated in disease. In this narrative review, we aimed to summarize the current evidence from observational and clinical trials involving the MedDiet by (1) assessing changes in the metabolome and microbiome for the measurement of diet pattern adherence and (2) assessing health outcomes related to the MedDiet through alterations to human metabolomics and/or the microbiome.

Metabolomics identifies increases in the acylcarnitine profiles in the plasma of overweight subjects in response to mild weight loss: a randomized, controlled design study

Background

Using metabolomics technique to analyze the response to a dietary intervention generates valuable information concerning the effects of the prescribed diet on metabolic regulation. To determine whether low calorie diet (LCD)-induced weight reduction causes changes in plasma metabolites and metabolic characteristics.

Methods

Overweight subjects consumed a LCD (n = 47) or a weight maintenance diet (control, n = 50) in a randomized, controlled design study with a 12-week clinical intervention period. Plasma samples were analyzed using an UPLC-LTQ-Orbitrap MS.

Results

The 12-week LCD intervention resulted in significant mild weight loss, with an 8.3% and 10.6% reduction observed in the visceral fat area (VFA) at the level of the lumbar vertebrae L1 and L4, respectively. The LCD group showed a significant increase in the mean change of serum free fatty acids compared to the control group. In the LCD group, we observed a significant increase in the acylcarnitine (AC) levels, including hexanoylcarnitine, L-octanoylcarnitine, 9-decenoylcarnitine, trans-2-dodecenoylcanitine, dodecanoylcarnitine, 3,5-tetradecadiencarnitine, cis-5-tetradecenoylcarnitine, 9,12-hexadecadienoylcarnitine, and 9-hexadecenoylcarnitne at the 12-week follow-up assessment. When the plasma metabolite changes from baseline were compared between the control and LCD groups, the LCD group showed significant increases in hexanoylcarnitine, L-octanoylcarnitine, trans-2-dodecenoylcanitine, and 3,5-tetradecadiencarnitine than the control group. Additionally, the changes in these ACs in the LCD group strongly negatively correlated with the changes in the VFA at L1 and/or L4.

Conclusion

Mild weight loss from 12-week calorie restriction increased the plasma levels of medium- and long-chain ACs. These changes were coupled with a decrease in VFA and an increase in free fatty acids.

Trial registration

NCT03135132; April 26, 2017.

Electronic supplementary material

The online version of this article (10.1186/s12944-018-0887-1) contains supplementary material, which is available to authorized users.

Combined systems pharmacology and fecal metabonomics to study the biomarkers and therapeutic mechanism of type 2 diabetic nephropathy treated with Astragalus and Leech

In our study, systems pharmacology was used to predict the molecular targets of Astragalus and Leech, and explore the therapeutic mechanism of type 2 diabetic nephropathy (T2DN) treated with Astragalus and Leech. Simultaneously, to reveal the systemic metabolic changes and biomarkers associated with T2DN, we performed 1H NMR-based metabonomics and multivariate analysis to analyze fecal samples obtained from model T2DN rats. In addition, ELISA kits and histopathological studies were used to examine biochemical parameters and kidney tissue, respectively. Striking differences in the Pearson's correlation of 22 biomarkers and 9 biochemical parameters were also observed among control, T2DN and treated rats. Results of systems pharmacology analysis revealed that 9 active compounds (3,9-di-O-methylnissolin; (6aR,11aR)-9,10-dimethoxy-6a,11a-dihydro-6H-benzofurano[3,2-c]chromen-3-ol; hirudin; l-isoleucine; phenylalanine; valine; hirudinoidine A-C) and 9 target proteins (l-serine dehydratase; 3-hydroxyacyl-CoA dehydrogenase; tyrosyl-tRNA synthetase; tryptophanyl-tRNA synthetase; branched-chain amino acid aminotransferase; acetyl-CoA C-acetyltransferase; isovaleryl-CoA dehydrogenase; pyruvate dehydrogenase E1 component alpha subunit; hydroxyacylglutathione hydrolase) of Astragalus and Leech were closely associated with the treatment of T2DN. Using fecal metabonomics analysis, 22 biomarkers were eventually found to be closely associated with the occurrence of T2DN. Combined with systems pharmacology and fecal metabonomics, these biomarkers were found to be mainly associated with 6 pathways, involving amino acid metabolism (leucine, valine, isoleucine, alanine, lysine, glutamate, taurine, phenylalanine, tryptophan); energy metabolism (lactate, succinate, creatinine, α-glucose, glycerol); ketone body and fatty acid metabolism (3-hydroxybutyrate, acetate, n-butyrate, propionate); methylamine metabolism (dimethylamine, trimethylamine); and secondary bile acid metabolism and urea cycle (deoxycholate, citrulline). The underlying mechanisms of action included protection of the liver and kidney, enhancement of insulin sensitivity and antioxidant activity, and improvement of mitochondrial function. To the best of our knowledge, this is the first time that systems pharmacology combined with fecal metabonomics has been used to study T2DN. 6 metabolites (n-butyrate, deoxycholate, propionate, tryptophan, taurine and glycerol) associated with T2DN were newly discovered in fecal samples. These 6 metabolites were mainly derived from the intestinal flora, and related to amino acid metabolism, fatty acid metabolism, and secondary bile acid metabolism. We hope the results of this study could be inspirational and helpful for further exploration of T2DN treatment. Meanwhile, our results highlighted that exploring the biomarkers of T2DN and therapeutic mechanisms of Traditional Chinese Medicine (TCM) formulas on T2DN by combining systems pharmacology and fecal metabonomics methods was a promising strategy.

Dietary methionine restriction regulated energy and protein homeostasis by improving thyroid function in high fat diet mice

Methionine-restricted diets (MRD) show an integrated series of beneficial health effects, including improving insulin sensitivity, limiting fat deposition, and decreasing oxidative stress, and inflammation responses. We aimed to explore the systemic responses to a MRD in mice fed with a high fat (HFD) and clarify the possible mechanism. Mice were fed with a control diet (0.86% methionine + 4% fat, CON), HFD (0.86% methionine + 20% fat), or MRD (0.17% methionine + 20% fat) for 22 consecutive weeks. HFD-fed mice showed widespread systemic metabolic disorders and thyroid dysfunction. A MRD significantly increased energy expenditure (e.g. fatty acid oxidation, glycolysis, and tricarboxylic acid cycle metabolism), regulated protein homeostasis, improved gut microbiota functions, prevented thyroid dysfunction, increased plasma thyroxine and triiodothyronine levels, decreased plasma thyroid stimulating hormone levels, increased type 2 deiodinase (DIO2) activity, and up-regulated mRNA and protein expression levels of DIO2 and thyroid hormone receptor α1 in the skeletal muscle. These results suggest that a MRD can improve the metabolic disorders induced by a HFD, and especially regulate energy and protein homeostasis likely through improved thyroid function. Thus, reducing methionine intake (e.g. through a vegan diet) may improve metabolic health in animals and humans.

Pre-clinical Pharmacokinetic and Metabolomic Analyses of Isorhapontigenin, a Dietary Resveratrol Derivative

Background: Isorhapontigenin (trans-3,5,4'-trihydroxy-3'-methoxystilbene, ISO), a dietary resveratrol (trans-3,5,4'-trihydroxystilbene) derivative, possesses various health-promoting activities. To further evaluate its medicinal potentials, the pharmacokinetic and metabolomic profiles of ISO were examined in Sprague-Dawley rats. Methods: The plasma pharmacokinetics and metabolomics were monitored by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and gas chromatography-tandem mass spectrometry (GC-MS/MS), respectively. Results: Upon intravenous injection (90 μmol/kg), ISO exhibited a fairly rapid clearance (CL) and short mean residence time (MRT). After a single oral administration (100 μmol/kg), ISO was rapidly absorbed and showed a long residence in the systemic circulation. Dose escalation to 200 μmol/kg resulted in higher dose-normalized maximal plasma concentrations (C_max/Dose), dose-normalized plasma exposures (AUC/Dose), and oral bioavailability (F). One-week repeated daily dosing of ISO did not alter its major oral pharmacokinetic parameters. Pharmacokinetic comparisons clearly indicated that ISO displayed pharmacokinetic profiles superior to resveratrol as its C_max/Dose, AUC/Dose, and F were approximately two to three folds greater than resveratrol. Metabolomic investigation revealed that 1-week ISO administration significantly reduced plasma concentrations of arachidonic acid, cholesterol, fructose, allantoin, and cadaverine but increased tryptamine levels, indicating its impact on metabolic pathways related to health-promoting effects. Conclusion: ISO displayed favorable pharmacokinetic profiles and may be a promising nutraceutical in view of its health-promoting properties.

Plasma metabolic profiling analysis of neurotoxicity induced by oxaliplatin using metabonomics and multivariate data analysis

Oxaliplatin is a third generation antitumor agent, which is often used in treating advanced colorectal cancer, but the use of oxaliplatin is limited by its side effects, especially peripheral nerve toxicity. Metabonomics techniques, as a holistic analytical technique, could provide basic information on the metabolic profile of biological fluids during drug administration. In this study, we used the ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) technique to analyze rat plasma samples collected seven days after oxaliplatin administration. The changes of metabolites in plasma samples were evaluated by principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA), and 15 kinds of neurotoxicity-related biomarkers were screened. The metabolic pathways of interference involved amino acid biosynthesis and metabolism, glycerophospholipid metabolism, sphingolipid metabolism and so on. The biomarkers found in this study are significant for the study of neurotoxicity.

The Effect of Lean-Seafood and Non-Seafood Diets on Fecal Metabolites and Gut Microbiome: Results from a Randomized Crossover Intervention Study

SCOPE

The impact of dietary protein types on the gut microbiome is scarcely studied. The aim of the present study is therefore to examine the effects of lean-seafood and non-seafood proteins on the gut microbiome composition and activity and elucidate potential associations to cardiovascular disease (CVD) risk factors.

METHODS

A crossover intervention study in which 20 healthy subjects consumed two diets that varied in protein source was conducted. ¹ H NMR spectroscopy and 16S rDNA sequencing analyses were applied to characterize fecal metabolites and gut microbiota composition, respectively.

RESULTS

A twofold increase in fecal trimethylamine excretion was observed after the lean-seafood diet period. Circulating TAG and the total to high-density lipoprotein (HDL) cholesterol ratio as well as circulating TMAO levels were each associated with specific gut bacteria. Following the non-seafood diet period, a decreased relative abundance of Clostridium cluster IV and a tendency toward an increased Firmicutes/Bacteroidetes ratio were found.

CONCLUSIONS

Lean-seafood and non-seafood diets differentially modulate the gut microbiome composition and activity. Furthermore, the gut microbiota composition seems to affect circulating TMAO levels and CVD risk factors.

Gut microbiota, fatty liver disease, and hepatocellular carcinoma

Intestinal bacteria contribute to the pathogenesis of non-alcoholic fatty liver disease (NAFLD). Recently developed microbial profiling techniques are beginning to shed light on the nature of the changes in the gut microbiota that accompany NAFLD and non-alcoholic steatohepatitis (NASH). In this review, we summarize the role of gut microbiota in the development of NAFLD, NASH, and hepatocellular carcinoma (HCC). We highlight the mechanisms by which gut microbiota contribute to NAFLD/NASH, including through alterations in gut epithelial permeability, choline metabolism, endogenous alcohol production, release of inflammatory cytokines, regulation of hepatic Toll-like receptor (TLR), and bile acid metabolism. In addition, we analyze possible mechanisms for enhanced hepatic carcinogenesis, including alterations in bile acid metabolism, release of inflammatory cytokines, and expression of TLR-4. Finally, we describe therapeutic approaches for NAFLD/NASH and preventive strategies for HCC involving modulation of the intestinal microbiota or affected host pathways. Although recent studies have provided useful information, large-scale prospective studies are required to better characterize the intestinal microbiota and metabolome, in order to demonstrate a causative role for changes in the gut microbiota in the etiology of NAFLD/NASH, to identify new therapeutic strategies for NAFLD/NASH, and to develop more effective methods of preventing HCC.

Use of Metabolomics in Improving Assessment of Dietary Intake

BACKGROUND

Nutritional metabolomics is rapidly evolving to integrate nutrition with complex metabolomics data to discover new biomarkers of nutritional exposure and status.

CONTENT

The purpose of this review is to provide a broad overview of the measurement techniques, study designs, and statistical approaches used in nutrition metabolomics, as well as to describe the current knowledge from epidemiologic studies identifying metabolite profiles associated with the intake of individual nutrients, foods, and dietary patterns.

SUMMARY

A wide range of technologies, databases, and computational tools are available to integrate nutritional metabolomics with dietary and phenotypic information. Biomarkers identified with the use of high-throughput metabolomics techniques include amino acids, acylcarnitines, carbohydrates, bile acids, purine and pyrimidine metabolites, and lipid classes. The most extensively studied food groups include fruits, vegetables, meat, fish, bread, whole grain cereals, nuts, wine, coffee, tea, cocoa, and chocolate. We identified 16 studies that evaluated metabolite signatures associated with dietary patterns. Dietary patterns examined included vegetarian and lactovegetarian diets, omnivorous diet, Western dietary patterns, prudent dietary patterns, Nordic diet, and Mediterranean diet. Although many metabolite biomarkers of individual foods and dietary patterns have been identified, those biomarkers may not be sensitive or specific to dietary intakes. Some biomarkers represent short-term intakes rather than long-term dietary habits. Nonetheless, nutritional metabolomics holds promise for the development of a robust and unbiased strategy for measuring diet. Still, this technology is intended to be complementary, rather than a replacement, to traditional well-validated dietary assessment methods such as food frequency questionnaires that can measure usual diet, the most relevant exposure in nutritional epidemiologic studies.

1H NMR and MVA metabolomic profiles of urines from piglets fed with boluses contaminated with a mixture of five mycotoxins

Metabolic profile of urine from piglets administered with single boluses contaminated with mycotoxin mixture (deoxynivalenol, aflatoxin B1, fumonisin B1, zearalenone, and ochratoxin A) were studied by 1H NMR spectroscopy and chemometrics (PCA, PLS-DA, and OPLS-DA). The mycotoxin levels were close to the established maximum and guidance levels for animal feed (2003/100/EC and 2006/576/EC). Urine samples were obtained from four groups of four piglets before (control, C) or within 24 h (treated, T) after receiving a contaminated boluses with increasing doses of mycotoxins (boluses 1-4). For the two highest dose groups, the urines were collected also after one week of wash out (W). For the two lowest doses groups no significant differences between the C and T samples were observed. By contrast, for the two highest doses groups the T urines separated from the controls for a higher relative content of creatinine, p-cresol glucuronide and phenyl acetyl glycine and lower concentration of betaine and TMAO. Interestingly, a similar profile was found for both W and T urines suggesting, at least for the highest doses used, serious alteration after a single bolus of mycotoxin mixture.

Multi-Omics Analysis Reveals a Correlation between the Host Phylogeny, Gut Microbiota and Metabolite Profiles in Cyprinid Fishes

Gut microbiota play key roles in host nutrition and metabolism. However, little is known about the relationship between host genetics, gut microbiota and metabolic profiles. Here, we used high-throughput sequencing and gas chromatography/mass spectrometry approaches to characterize the microbiota composition and the metabolite profiles in the gut of five cyprinid fish species with three different feeding habits raised under identical husbandry conditions. Our results showed that host species and feeding habits significantly affect not only gut microbiota composition but also metabolite profiles (ANOSIM, p ≤ 0.05). Mantel test demonstrated that host phylogeny, gut microbiota, and metabolite profiles were significantly related to each other (p ≤ 0.05). Additionally, the carps with the same feeding habits had more similarity in gut microbiota composition and metabolite profiles. Various metabolites were correlated positively with bacterial taxa involved in food degradation. Our results shed new light on the microbiome and metabolite profiles in the gut content of cyprinid fishes, and highlighted the correlations between host genotype, fish gut microbiome and putative functions, and gut metabolite profiles.

Integration of Traditional and Metabolomics Biomarkers Identifies Prognostic Metabolites for Predicting Responsiveness to Nutritional Intervention against Oxidative Stress and Inflammation

Various statistical approaches can be applied to integrate traditional and omics biomarkers, allowing the discovery of prognostic markers to classify subjects into poor and good prognosis groups in terms of responses to nutritional interventions. Here, we performed a prototype study to identify metabolites that predict responses to an intervention against oxidative stress and inflammation, using a data set from a randomized controlled trial evaluating Korean black raspberry (KBR) in sedentary overweight/obese subjects. First, a linear mixed-effects model analysis with multiple testing correction showed that four-week consumption of KBR significantly changed oxidized glutathione (GSSG, q = 0.027) level, the ratio of reduced glutathione (GSH) to GSSG (q = 0.039) in erythrocytes, malondialdehyde (MDA, q = 0.006) and interleukin-6 (q = 0.006) levels in plasma, and seventeen NMR metabolites in urine compared with those in the placebo group. A subsequent generalized linear mixed model analysis showed linear correlations between baseline urinary glycine and N-phenylacetylglycine (PAG) and changes in the GSH:GSSG ratio (p = 0.008 and 0.004) as well as between baseline urinary adenine and changes in MDA (p = 0.018). Then, receiver operating characteristic analysis revealed that a two-metabolite set (glycine and PAG) had the strongest prognostic relevance for future interventions against oxidative stress (the area under the curve (AUC) = 0.778). Leave-one-out cross-validation confirmed the accuracy of prediction (AUC = 0.683). The current findings suggest that a higher level of this two-metabolite set at baseline is useful for predicting responders to dietary interventions in subjects with oxidative stress and inflammation, contributing to the emergence of personalized nutrition.

Metabolomics, Nutrition, and Potential Biomarkers of Food Quality, Intake, and Health Status

Diet, dietary patterns, and other environmental factors such as exposure to toxins are playing an important role in the prevention/development of many diseases, like obesity, type 2 diabetes, and consequently on the health status of individuals. A major challenge nowadays is to identify novel biomarkers to detect as early as possible metabolic dysfunction and to predict evolution of health status in order to refine nutritional advices to specific population groups. Omics technologies such as genomics, transcriptomics, proteomics, and metabolomics coupled with statistical and bioinformatics tools have already shown great potential in this research field even if so far only few biomarkers have been validated. For the past two decades, important analytical techniques have been developed to detect as many metabolites as possible in human biofluids such as urine, blood, and saliva. In the field of food science and nutrition, many studies have been carried out for food authenticity, quality, and safety, as well as for food processing. Furthermore, metabolomic investigations have been carried out to discover new early biomarkers of metabolic dysfunction and predictive biomarkers of developing pathologies (obesity, metabolic syndrome, type-2 diabetes, etc.). Great emphasis is also placed in the development of methodologies to identify and validate biomarkers of nutrients exposure.

Metabolomic studies on the systemic responses of mice with oxidative stress induced by short-term oxidized tyrosine administration

Oxidized tyrosine (O-Tyr) has attracted more interest in recent years because many researchers have discovered that it and its product (dityrosine) are associated with pathological conditions, especially various age-related disorders in biological systems.

Nontargeted LC-MS Metabolomics Approach for Metabolic Profiling of Plasma and Urine from Pigs Fed Branched Chain Amino Acids for Maximum Growth Performance

The metabolic response in plasma and urine of pigs when feeding an optimum level of branched chain amino acids (BCAAs) for best growth performance is unknown. The objective of the current study was to identify the metabolic phenotype associated with the BCAAs intake level that could be linked to the animal growth performance. Three dose-response studies were carried out to collect blood and urine samples from pigs fed increasing levels of Ile, Val, or Leu followed by a nontargeted LC-MS approach to characterize the metabolic profile of biofluids when dietary BCAAs are optimum for animal growth. Results showed that concentrations of plasma hypoxanthine and tyrosine (Tyr) were higher while concentrations of glycocholic acid, tauroursodeoxycholic acid, and taurocholic acid were lower when the dietary Ile was optimum. Plasma 3-methyl-2-oxovaleric acid and creatine were lower when dietary Leu was optimum. The optimum dietary Leu resulted in increased urinary excretion of ascorbic acid and choline and relatively decreased excretion of 2-aminoadipic acid, acetyl-dl-valine, Ile, 2-methylbutyrylglycine, and Tyr. In conclusion, plasma glycocholic acid and taurocholic acid were discriminating metabolites to the optimum dietary Ile. The optimum dietary Leu was associated with reduced plasma creatine and urinary 2-aminoadipic acid and elevated urinary excretion of ascorbic acid and choline. The optimum dietary Val had a less pronounced metabolic response reflected in plasma or urine than other BCAA.

Computational Metabolomics: A Framework for the Million Metabolome

"Sola dosis facit venenum." These words of Paracelsus, "the dose makes the poison", can lead to a cavalier attitude concerning potential toxicities of the vast array of low abundance environmental chemicals to which humans are exposed. Exposome research teaches that 80-85% of human disease is linked to environmental exposures. The human exposome is estimated to include >400,000 environmental chemicals, most of which are uncharacterized with regard to human health. In fact, mass spectrometry measures >200,000 m/z features (ions) in microliter volumes derived from human samples; most are unidentified. This crystallizes a grand challenge for chemical research in toxicology: to develop reliable and affordable analytical methods to understand health impacts of the extensive human chemical experience. To this end, there appears to be no choice but to abandon the limitations of measuring one chemical at a time. The present review looks at progress in computational metabolomics to provide probability-based annotation linking ions to known chemicals and serve as a foundation for unambiguous designation of unidentified ions for toxicologic study. We review methods to characterize ions in terms of accurate mass m/z, chromatographic retention time, correlation of adduct, isotopic and fragment forms, association with metabolic pathways and measurement of collision-induced dissociation products, collision cross section, and chirality. Such information can support a largely unambiguous system for documenting unidentified ions in environmental surveillance and human biomonitoring. Assembly of this data would provide a resource to characterize and understand health risks of the array of low-abundance chemicals to which humans are exposed.

Combining NMR and LC/MS Using Backward Variable Elimination: Metabolomics Analysis of Colorectal Cancer, Polyps, and Healthy Controls

Both nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) play important roles in metabolomics. The complementary features of NMR and MS make their combination very attractive; however, currently the vast majority of metabolomics studies use either NMR or MS separately, and variable selection that combines NMR and MS for biomarker identification and statistical modeling is still not well developed. In this study focused on methodology, we developed a backward variable elimination partial least-squares discriminant analysis algorithm embedded with Monte Carlo cross validation (MCCV-BVE-PLSDA), to combine NMR and targeted liquid chromatography (LC)/MS data. Using the metabolomics analysis of serum for the detection of colorectal cancer (CRC) and polyps as an example, we demonstrate that variable selection is vitally important in combining NMR and MS data. The combined approach was better than using NMR or LC/MS data alone in providing significantly improved predictive accuracy in all the pairwise comparisons among CRC, polyps, and healthy controls. Using this approach, we selected a subset of metabolites responsible for the improved separation for each pairwise comparison, and we achieved a comprehensive profile of altered metabolite levels, including those in glycolysis, the TCA cycle, amino acid metabolism, and other pathways that were related to CRC and polyps. MCCV-BVE-PLSDA is straightforward, easy to implement, and highly useful for studying the contribution of each individual variable to multivariate statistical models. On the basis of these results, we recommend using an appropriate variable selection step, such as MCCV-BVE-PLSDA, when analyzing data from multiple analytical platforms to obtain improved statistical performance and a more accurate biological interpretation, especially for biomarker discovery. Importantly, the approach described here is relatively universal and can be easily expanded for combination with other analytical technologies.

A metabonomic investigation on the biochemical perturbation in post-stroke patients with depressive disorder (PSD)

A metabonomics study based on GC/MS and multivariate statistical analysis was performed involving 28 post stroke depressed (PSD) patients, 27 post-stroke non-depressed (PSND) patients and 33 healthy subjects to investigate the biochemical perturbation in their plasma samples. The outcome of this study showed that there was distinctive metabolic profile for PSD patients. Seven sentinel metabolites showed marked perturbations in PSD patients' blood. The introduction of metabonomics approach may provide a novel metabonomic insight about PSD and the sentinel metabolites for classifying PSD.

The Healthy Core Metabolism: A New Paradigm for Primary Preventive Nutrition

Research in preventive nutrition aims at elucidating mechanism by which our diet helps us to remain in good health through optimal physiological functions. However, despite decades of accumulated data in human nutrition and regular subsequent nutritional recommendations, obesity and type 2 diabetes epidemics continue to progress worldwide each year leading to a regular decrease of the Healthy Life Years, notably in Western countries. Such a paradox may be explained by the Nutrition Transition, the extreme application of the reductionist paradigm in nutrition research, the lack of nutritional education and a too strong focus on curative nutrition in at risk/ill subjects. In this position paper, we hypothesized that researchers should focus more on healthy subjects, from birth until maturity. Rather than exploring what differentiates healthy and at risk/ill subjects, we propose to thoroughly study what characterizes a healthy state and its underlying metabolism. We define it as the Healthy Core Metabolism which remains stable whatever energy inputs (diets) and outputs (exercise), genetic background and external/internal stress, e.g., temporary illnesses. As a basis for Healthy Core Metabolism investigation, we observed that main physiological and ubiquitous functions of human organism, i.e., the neuro-vasculo-sarco-osteoporotic system, tend to follow a concave curve with common phases of growth, optimum, and decline. Finally, we hypothesized that true primary preventive nutrition should focus on the growth phase to reach the maximum capital of a given physiological function so that - whatever the further decline -, Healthy Life Years may approach or coincide with theoretical Life Expectancy.

Effects of glutamine against oxidative stress in the metabolome of rats—new insight

Glutamine exerts potential functions against the harmful effects of oxidative stress on animals.

Globally Optimized Targeted Mass Spectrometry: Reliable Metabolomics Analysis with Broad Coverage

Targeted detection is one of the most important methods in mass spectrometry (MS)-based metabolomics; however, its major limitation is the reduced metabolome coverage that results from the limited set of targeted metabolites typically used in the analysis. In this study we describe a new approach, globally optimized targeted (GOT)-MS, that combines many of the advantages of targeted detection and global profiling in metabolomics analysis, including the capability to detect unknowns, broad metabolite coverage, and excellent quantitation. The key step in GOT-MS is a global search of precursor and product ions using a single liquid chromatography-triple quadrupole (LC-QQQ) mass spectrometer. Here, focused on measuring serum metabolites, we obtained 595 precursor ions and 1 890 multiple reaction monitoring (MRM) transitions, under positive and negative ionization modes in the mass range of 60-600 Da. For many of the MRMs/metabolites under investigation, the analytical performance of GOT-MS is better than or at least comparable to that obtained by global profiling using a quadrupole-time-of-flight (Q-TOF) instrument of similar vintage. Using a study of serum metabolites in colorectal cancer (CRC) as a representative example, GOT-MS significantly outperformed a large targeted MS assay containing ∼160 biologically important metabolites and provided a complementary approach to traditional global profiling using Q-TOF-MS. GOT-MS thus expands and optimizes the detection capabilities for QQQ-MS through a novel approach and should have the potential to significantly advance both basic and clinical metabolic research.