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1.
Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians.
Allaband, C, McDonald, D, Vázquez-Baeza, Y, Minich, JJ, Tripathi, A, Brenner, DA, Loomba, R, Smarr, L, Sandborn, WJ, Schnabl, B, et al
Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association. 2019;(2):218-230
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Abstract
Advances in technical capabilities for reading complex human microbiomes are leading to an explosion of microbiome research, leading in turn to intense interest among clinicians in applying these techniques to their patients. In this review, we discuss the content of the human microbiome, including intersubject and intrasubject variability, considerations of study design including important confounding factors, and different methods in the laboratory and on the computer to read the microbiome and its resulting gene products and metabolites. We highlight several common pitfalls for clinicians, including the expectation that an individual's microbiome will be stable, that diet can induce rapid changes that are large compared with the differences among subjects, that everyone has essentially the same core stool microbiome, and that different laboratory and computational methods will yield essentially the same results. We also highlight the current limitations and future promise of these techniques, with the expectation that an understanding of these considerations will help accelerate the path toward routine clinical application of these techniques developed in research settings.
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Applications of Innovative Lipidomic Methods for Blood Lipid Biomarkers.
Stark, KD
Journal of oleo science. 2019;(6):503-510
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Abstract
Assessing dietary intake is critical for understanding the relationship between diet and health. Fatty acid blood biomarkers have been particularly useful in determining dietary intakes and assessing the risk of chronic disease. However, fatty acid analysis involves the removal of fatty acids from their complex lipid structures resulting in a loss of potentially useful biological information. "Lipidomics" involves the use of mass spectrometry to identify lipids in their native form. Lipidomic approaches present challenges as an alternative to fatty acid analysis. This includes different types of lipidomic approaches and a lack of consensus on the lipids reported in different studies. Distinguishing between macrolipidomic approaches to characterize highly abundant lipids and microlipidomic approaches examining low abundant bioactive lipids and the use of brutto, medio, genio, and infinio to describe the level of information of lipidomic data can provide clarity to the field. Using lipidomic measurements for understanding docosahexaenoic acid metabolism during pregnancy will also be examined.
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A Metabonomics Approach to Drug Toxicology in Liver Disease and its Application in Traditional Chinese Medicine.
Su, G, Wang, H, Bai, J, Chen, G, Pei, Y
Current drug metabolism. 2019;(4):292-300
Abstract
BACKGROUND The progression of liver disease causes metabolic transformation in vivo and thus affects corresponding endogenous small molecular compounds. Metabonomics is a powerful technology which is able to assess global low-molecular-weight endogenous metabolites in a biological system. This review is intended to provide an overview of a metabonomics approach to the drug toxicology of diseases of the liver. METHODS The regulation of, and relationship between, endogenous metabolites and diseases of the liver is discussed in detail. Furthermore, the metabolic pathways involved in drug interventions of liver diseases are reviewed. Evaluation of the protective mechanisms of traditional Chinese medicine in liver diseases using metabonomics is also reviewed. Examples of applications of metabolite profiling concerning biomarker discovery are highlighted. In addition, new developments and future prospects are described. RESULTS Metabonomics can measure changes in metabolism relating to different stages of liver disease, so metabolic differences can provide a basis for the diagnosis, treatment and prognosis of various diseases. CONCLUSION Metabonomics has great advantages in all aspects of the therapy of liver diseases, with good prospects for clinical application.
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Factors influencing the cardiometabolic response to (poly)phenols and phytosterols: a review of the COST Action POSITIVe activities.
Gibney, ER, Milenkovic, D, Combet, E, Ruskovska, T, Greyling, A, González-Sarrías, A, de Roos, B, Tomás-Barberán, F, Morand, C, Rodriguez-Mateos, A
European journal of nutrition. 2019;(Suppl 2):37-47
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Abstract
PURPOSE Evidence exists regarding the beneficial effects of diets rich in plant-based foods regarding the prevention of cardiometabolic diseases. These plant-based foods are an exclusive and abundant source of a variety of biologically active phytochemicals, including polyphenols, carotenoids, glucosinolates and phytosterols, with known health-promoting effects through a wide range of biological activities, such as improvements in endothelial function, platelet function, blood pressure, blood lipid profile and insulin sensitivity. We know that an individual's physical/genetic makeup may influence their response to a dietary intervention, and thereby may influence the benefit/risk associated with consumption of a particular dietary constituent. This inter-individual variation in responsiveness has also been described for dietary plant bioactives but has not been explored in depth. To address this issue, the European scientific experts involved in the COST Action POSITIVe systematically analyzed data from published studies to assess the inter-individual variation in selected clinical biomarkers associated with cardiometabolic risk, in response to the consumption of plant-based bioactives (poly)phenols and phytosterols. The present review summarizes the main findings resulting from the meta-analyses already completed. RESULTS Meta-analyses of randomized controlled trials conducted within POSITIVe suggest that age, sex, ethnicity, pathophysiological status and medication may be responsible for the heterogeneity in the biological responsiveness to (poly)phenol and phytosterol consumption and could lead to inconclusive results in some clinical trials aiming to demonstrate the health effects of specific dietary bioactive compounds. However, the contribution of these factors is not yet demonstrated consistently across all polyphenolic groups and cardiometabolic outcomes, partly due to the heterogeneity in trial designs, low granularity of data reporting, variety of food vectors and target populations, suggesting the need to implement more stringent reporting practices in the future studies. Studies investigating the effects of genetic background or gut microbiome on variability were limited and should be considered in future studies. CONCLUSION Understanding why some bioactive plant compounds work effectively in some individuals but not, or less, in others is crucial for a full consideration of these compounds in future strategies of personalized nutrition for a better prevention of cardiometabolic disease. However, there is also still a need for the development of a substantial evidence-base to develop health strategies, food products or lifestyle solutions that embrace this variability.
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Nutrimetabolomics: An Integrative Action for Metabolomic Analyses in Human Nutritional Studies.
Ulaszewska, MM, Weinert, CH, Trimigno, A, Portmann, R, Andres Lacueva, C, Badertscher, R, Brennan, L, Brunius, C, Bub, A, Capozzi, F, et al
Molecular nutrition & food research. 2019;(1):e1800384
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Abstract
The life sciences are currently being transformed by an unprecedented wave of developments in molecular analysis, which include important advances in instrumental analysis as well as biocomputing. In light of the central role played by metabolism in nutrition, metabolomics is rapidly being established as a key analytical tool in human nutritional studies. Consequently, an increasing number of nutritionists integrate metabolomics into their study designs. Within this dynamic landscape, the potential of nutritional metabolomics (nutrimetabolomics) to be translated into a science, which can impact on health policies, still needs to be realized. A key element to reach this goal is the ability of the research community to join, to collectively make the best use of the potential offered by nutritional metabolomics. This article, therefore, provides a methodological description of nutritional metabolomics that reflects on the state-of-the-art techniques used in the laboratories of the Food Biomarker Alliance (funded by the European Joint Programming Initiative "A Healthy Diet for a Healthy Life" (JPI HDHL)) as well as points of reflections to harmonize this field. It is not intended to be exhaustive but rather to present a pragmatic guidance on metabolomic methodologies, providing readers with useful "tips and tricks" along the analytical workflow.
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Harnessing microbial metabolomics for industrial applications.
Zhao, J, Wang, G, Chu, J, Zhuang, Y
World journal of microbiology & biotechnology. 2019;(1):1
Abstract
Metabolome defines a set of metabolites present in a biological sample, which provides an immediate and dynamic recording of microbes in response to genetic and/or environmental perturbations. In recent years, metabolomics in combination with other omics diagnostic tools such as genomics, transcriptomics and proteomics is focused on addressing open biological questions that accelerate our understanding of the system as a whole and boost the use of systems metabolic engineering tools in industrial settings. In this review article, we summarize the applications of metabolomics to industrial microbial fermentations with respect to the bulk production of organic acids, amino acids, enzymes, antibiotics and therapeutic proteins. In addition, future prospects regarding metabolomics-assisted research are provided.
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Advances in Research on Diabetes by Human Nutriomics.
Ren, X, Li, X
International journal of molecular sciences. 2019;(21)
Abstract
The incidence and prevalence of diabetes mellitus (DM) have increased rapidly worldwide over the last two decades. Because the pathogenic factors of DM are heterogeneous, determining clinically effective treatments for DM patients is difficult. Applying various nutrient analyses has yielded new insight and potential treatments for DM patients. In this review, we summarized the omics analysis methods, including nutrigenomics, nutritional-metabolomics, and foodomics. The list of the new targets of SNPs, genes, proteins, and gut microbiota associated with DM has been obtained by the analysis of nutrigenomics and microbiomics within last few years, which provides a reference for the diagnosis of DM. The use of nutrient metabolomics analysis can obtain new targets of amino acids, lipids, and metal elements, which provides a reference for the treatment of DM. Foodomics analysis can provide targeted dietary strategies for DM patients. This review summarizes the DM-associated molecular biomarkers in current applied omics analyses and may provide guidance for diagnosing and treating DM.
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The potentiality of NMR-based metabolomics in food science and food authentication assessment.
Consonni, R, Cagliani, LR
Magnetic resonance in chemistry : MRC. 2019;(9):558-578
Abstract
In the last years, there was an increasing interest on nuclear magnetic resonance (NMR) spectroscopy, whose applications experienced an exponential growth in several research fields, particularly in food science. NMR was initially developed as the elective technique for structure elucidation of single molecules and nowadays is playing a dominant role in complex mixtures investigations. In the era of the "omics" techniques, NMR was rapidly enrolled as one of the most powerful methods to approach metabolomics studies. Its use in analytical routines, characterized by rapid and reproducible measurements, would provide the identification of a wide range of chemical compounds simultaneously, disclosing sophisticated frauds or addressing the geographical origin, as well as revealing potential markers for other authentication purposes. The great economic value of high-quality or guaranteed foods demands highly detailed characterization to protect both consumers and producers from frauds. The present scenario suggests metabolomics as the privileged approach of modern analytical studies for the next decades. The large potentiality of high-resolution NMR techniques is here presented through specific applications and using different approaches focused on the authentication process of some foods, like tomato paste, saffron, honey, roasted coffee, and balsamic and traditional balsamic vinegar of Modena, with a particular focus on geographical origin characterization, ageing determination, and fraud detection.
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Metabolic interactions in asthma.
Farraia, M, Cavaleiro Rufo, J, Paciência, I, Castro Mendes, F, Delgado, L, Laerte Boechat, J, Moreira, A
European annals of allergy and clinical immunology. 2019;(5):196-205
Abstract
Metabolomics can be used to explore altered metabolic pathways in asthma, giving insights into its pathophysiology. We aimed to review how metabolomics has been used to understand asthma by describing metabolic pathways under research and discussing clinical implications. The search was performed in PubMed, and studies published since 2000 using a metabolomics approach, were included. A total of 32 studies were analysed. Pathways related with cellular energy homeostasis, lipid metabolism and oxidative stress, immune and inflammatory processes and others were altered. Initial studies focused on biomarker discovery. But, metabolomics can be used to evaluate drug effects on specific pathways, to highlight pathways that can further develop in new targeted treatments and to identify differences according to asthma severity and phenotypes.
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Metabolic phenotyping of malnutrition during the first 1000 days of life.
Mayneris-Perxachs, J, Swann, JR
European journal of nutrition. 2019;(3):909-930
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Abstract
Nutritional restrictions during the first 1000 days of life can impair or delay the physical and cognitive development of the individual and have long-term consequences for their health. Metabolic phenotyping (metabolomics/metabonomics) simultaneously measures a diverse range of low molecular weight metabolites in a sample providing a comprehensive assessment of the individual's biochemical status. There are a growing number of studies applying such approaches to characterize the metabolic derangements induced by various forms of early-life malnutrition. This includes acute and chronic undernutrition and specific micronutrient deficiencies. Collectively, these studies highlight the diverse and dynamic metabolic disruptions resulting from various forms of nutritional deficiencies. Perturbations were observed in many pathways including those involved in energy, amino acid, and bile acid metabolism, the metabolic interactions between the gut microbiota and the host, and changes in metabolites associated with gut health. The information gleaned from such studies provides novel insights into the mechanisms linking malnutrition with developmental impairments and assists in the elucidation of candidate biomarkers to identify individuals at risk of developmental shortfalls. As the metabolic profile represents a snapshot of the biochemical status of an individual at a given time, there is great potential to use this information to tailor interventional strategies specifically to the metabolic needs of the individual.