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Molecules (Basel, Switzerland) Jun 2019Metabolomics is a powerful tool used to understand comprehensive changes in the metabolic response and to study the phenotype of an organism by instrumental analysis. It... (Meta-Analysis)
Meta-Analysis Review
Metabolomics is a powerful tool used to understand comprehensive changes in the metabolic response and to study the phenotype of an organism by instrumental analysis. It most commonly involves mass spectrometry followed by data mining and metabolite assignment. For the last few decades, hair has been used as a valuable analytical sample to investigate retrospective xenobiotic exposure as it provides a wider window of detection than other biological samples such as saliva, plasma, and urine. Hair contains functional metabolomes such as amino acids and lipids. Moreover, segmental analysis of hair based on its growth rate can provide information on metabolic changes over time. Therefore, it has great potential as a metabolomics sample to monitor chronic diseases, including drug addiction or abnormal conditions. In the current review, the latest applications of hair metabolomics in animal studies and clinical settings are highlighted. For this purpose, we review and discuss the characteristics of hair as a metabolomics sample, the analytical techniques employed in hair metabolomics and the consequence of hair metabolome alterations in recent studies. Through this, the value of hair as an alternative biological sample in metabolomics is highlighted.
Topics: Animals; Chromatography, High Pressure Liquid; Hair; Humans; Mass Spectrometry; Metabolome; Metabolomics
PubMed: 31212725
DOI: 10.3390/molecules24122195 -
Wiley Interdisciplinary Reviews.... 2015The human gut microbiota performs essential functions for host and well-being, but has also been linked to a variety of disease states, e.g., obesity and type 2... (Review)
Review
The human gut microbiota performs essential functions for host and well-being, but has also been linked to a variety of disease states, e.g., obesity and type 2 diabetes. The mammalian body fluid and tissue metabolomes are greatly influenced by the microbiota, with many health-relevant metabolites being considered 'mammalian-microbial co-metabolites'. To systematically investigate this complex host-microbial co-metabolism, a systems biology approach integrating high-throughput data and computational network models is required. Here, we review established top-down and bottom-up systems biology approaches that have successfully elucidated relationships between gut microbiota-derived metabolites and host health and disease. We focus particularly on the constraint-based modeling and analysis approach, which enables the prediction of mechanisms behind metabolic host-microbe interactions on the molecular level. We illustrate that constraint-based models are a useful tool for the contextualization of metabolomic measurements and can further our insight into host-microbe interactions, yielding, e.g., in potential novel drugs and biomarkers.
Topics: Animals; Body Fluids; Gastrointestinal Tract; Host-Pathogen Interactions; Humans; Metabolome; Metabolomics; Microbiota; Models, Biological
PubMed: 25929487
DOI: 10.1002/wsbm.1301 -
Advances in Experimental Medicine and... 2023Highly selective and sensitive analytical techniques are necessary for microbial metabolomics due to the complexity of the microbial sample matrix. Hence, mass...
Highly selective and sensitive analytical techniques are necessary for microbial metabolomics due to the complexity of the microbial sample matrix. Hence, mass spectrometry (MS) has been successfully applied in microbial metabolomics due to its high precision, versatility, sensitivity, and wide dynamic range. The different analytical tools using MS have been employed in microbial metabolomics investigations and can contribute to the discovery or accelerate the search for bioactive substances. The coupling with chromatographic and electrophoretic separation techniques has resulted in more efficient technologies for the analysis of microbial compounds occurring in trace levels. This book chapter describes the current advances in the application of mass spectrometry-based metabolomics in the search for new biologically active agents from microbial sources; the development of new approaches for in silico annotation of natural products; the different technologies employing mass spectrometry imaging to deliver more comprehensive analysis and elucidate the metabolome involved in ecological interactions as they enable visualization of the spatial dispersion of small molecules. We also describe other ambient ionization techniques applied to the fingerprint of microbial natural products and modern techniques such as ion mobility mass spectrometry used to microbial metabolomic analyses and the dereplication of natural microbial products through MS.
Topics: Mass Spectrometry; Metabolomics; Metabolome; Biological Products
PubMed: 37843807
DOI: 10.1007/978-3-031-41741-2_5 -
Current Opinion in Chemical Biology Feb 2020Understanding the molecular mechanisms of endogenous and environmental metabolites is crucial for basic biology and drug discovery. With the genome, proteome, and... (Review)
Review
Understanding the molecular mechanisms of endogenous and environmental metabolites is crucial for basic biology and drug discovery. With the genome, proteome, and metabolome of many organisms being readily available, researchers now have the opportunity to dissect how key metabolites regulate complex cellular pathways in vivo. Nonetheless, characterizing the specific and functional protein targets of key metabolites associated with specific cellular phenotypes remains a major challenge. Innovations in chemical biology are now poised to address this fundamental limitation in physiology and disease. In this review, we highlight recent advances in chemoproteomics for targeted and proteome-wide analysis of metabolite-protein interactions that have enabled the discovery of unpredicted metabolite-protein interactions and facilitated the development of new small molecule therapeutics.
Topics: Humans; Metabolome; Metabolomics; Proteins; Proteome; Proteomics
PubMed: 31790852
DOI: 10.1016/j.cbpa.2019.10.008 -
International Journal of Molecular... Jun 2018A new era of plant biochemistry at the systems level is emerging, providing detailed descriptions of biochemical phenomena at the cellular and organismal level. This new... (Review)
Review
A new era of plant biochemistry at the systems level is emerging, providing detailed descriptions of biochemical phenomena at the cellular and organismal level. This new era is marked by the advent of metabolomics—the qualitative and quantitative investigation of the entire metabolome (in a dynamic equilibrium) of a biological system. This field has developed as an indispensable methodological approach to study cellular biochemistry at a global level. For protection and survival in a constantly-changing environment, plants rely on a complex and multi-layered innate immune system. This involves surveillance of ‘self’ and ‘non-self,’ molecule-based systemic signalling and metabolic adaptations involving primary and secondary metabolites as well as epigenetic modulation mechanisms. Establishment of a pre-conditioned or primed state can sensitise or enhance aspects of innate immunity for faster and stronger responses. Comprehensive elucidation of the molecular and biochemical processes associated with the phenotypic defence state is vital for a better understanding of the molecular mechanisms that define the metabolism of plant⁻pathogen interactions. Such insights are essential for translational research and applications. Thus, this review highlights the prospects of metabolomics and addresses current challenges that hinder the realisation of the full potential of the field. Such limitations include partial coverage of the metabolome and maximising the value of metabolomics data (extraction of information and interpretation). Furthermore, the review points out key features that characterise both the plant innate immune system and enhancement of the latter, thus underlining insights from metabolomic studies in plant priming. Future perspectives in this inspiring area are included, with the aim of stimulating further studies leading to a better understanding of plant immunity at the metabolome level.
Topics: Adaptation, Physiological; Crop Production; Epigenesis, Genetic; Metabolome; Metabolomics; Plant Immunity; Plant Physiological Phenomena; Plants
PubMed: 29899301
DOI: 10.3390/ijms19061759 -
Journal of Magnetic Resonance (San... Sep 2019NMR has been used to perform metabolic studies, metabolic profiling and metabolomics in biofluids and tissues for more than 40 years. This close connection between... (Review)
Review
NMR has been used to perform metabolic studies, metabolic profiling and metabolomics in biofluids and tissues for more than 40 years. This close connection between metabolic measurements and NMR has flourished because of NMR's many unique strengths for characterizing the chemical composition of complex mixtures. However, a number of other technologies, including mass spectrometry, have appeared in the past few years that are encroaching on NMR's dominance in metabolomics and metabolic studies. In this brief review, some of the current strengths and existing limitations of NMR-based metabolomics are highlighted. Additionally, a number of recent advances in NMR hardware, methodology and software are also described and these advancements are used to speculate about where NMR-based metabolomics is going, what needs to be done to make it more popular and how it will evolve in the next 5-10 years.
Topics: Animals; Humans; Metabolome; Metabolomics; Nuclear Magnetic Resonance, Biomolecular
PubMed: 31377153
DOI: 10.1016/j.jmr.2019.07.013 -
Advances in Clinical Chemistry 2022Metabolism is a highly regulated process that provides nutrients to cells and essential building blocks for the synthesis of protein, DNA and other macromolecules. In... (Review)
Review
Metabolism is a highly regulated process that provides nutrients to cells and essential building blocks for the synthesis of protein, DNA and other macromolecules. In healthy biological systems, metabolism maintains a steady state in which the concentrations of metabolites are relatively constant yet are subject to metabolic demands and environmental stimuli. Rare genetic disorders, such as inborn errors of metabolism (IEM), cause defects in regulatory enzymes or proteins leading to metabolic pathway disruption and metabolite accumulation or deficiency. Traditionally, the laboratory diagnosis of IEMs has been limited to analytical methods that target specific metabolites such as amino acids and acyl carnitines. This approach is effective as a screening method for the most common IEM disorders but lacks the comprehensive coverage of metabolites that is necessary to identify rare disorders that present with nonspecific clinical symptoms. Fortunately, advancements in technology and data analytics has introduced a new field of study called metabolomics which has allowed scientists to perform comprehensive metabolite profiling of biological systems to provide insight into mechanism of action and gene function. Since metabolomics seeks to measure all small molecule metabolites in a biological specimen, it provides an innovative approach to evaluating disease in patients with rare genetic disorders. In this review we provide insight into the appropriate application of metabolomics in clinical settings. We discuss the advantages and limitations of the method and provide details related to the technology, data analytics and statistical modeling required for metabolomic profiling of patients with IEMs.
Topics: Biomarkers; Humans; Metabolic Networks and Pathways; Metabolism, Inborn Errors; Metabolome; Metabolomics
PubMed: 35337606
DOI: 10.1016/bs.acc.2021.09.001 -
CNS Spectrums Jun 2019Approximately 20%-30% of schizophrenia patients are resistant to current standard pharmacotherapies. Recent schizophrenia research aims to identify specific... (Review)
Review
Approximately 20%-30% of schizophrenia patients are resistant to current standard pharmacotherapies. Recent schizophrenia research aims to identify specific pathophysiological abnormalities and novel targets in the disease, with the goals of identifying at-risk individuals, facilitating diagnosis, prompting early and personalized interventions, and helping predict response to treatment. Metabolomics involves the systematic study of the profile of biochemical alterations early in the course of a given disorder. Major aspects of the schizophrenia metabolome have been characterized, uncovering potential selective biomarkers for the disease that may change how the disorder is diagnosed, and how patients are stratified and treated. This review focuses on the most common metabolomic fingerprints of the different pathways involved in the pathophysiology of schizophrenia, and the potential development of novel metabolomic-related pharmacotherapies for improved treatment of schizophrenia and other related idiopathic psychotic disorders.
Topics: Animals; Antipsychotic Agents; Drug Discovery; Humans; Metabolome; Metabolomics; Schizophrenia
PubMed: 29866209
DOI: 10.1017/S1092852918000962 -
Molecules (Basel, Switzerland) Nov 2023Wine has a rich history dating back to 2200 BC, originally recognized for its medicinal properties. Today, with the aid of advanced technologies like metabolomics and... (Review)
Review
Wine has a rich history dating back to 2200 BC, originally recognized for its medicinal properties. Today, with the aid of advanced technologies like metabolomics and sophisticated analytical techniques, we have gained remarkable insights into the molecular-level changes induced by wine consumption in the human organism. This review embarks on a comprehensive exploration of the alterations in human metabolome associated with wine consumption. A great number of 51 studies from the last 25 years were reviewed; these studies systematically investigated shifts in metabolic profiles within blood, urine, and feces samples, encompassing both short-term and long-term studies of the consumption of wine and wine derivatives. Significant metabolic alterations were observed in a wide variety of metabolites belonging to different compound classes, such as phenolic compounds, lipids, organic acids, and amino acids, among others. Within these classes, both endogenous metabolites as well as diet-related metabolites that exhibited up-regulation or down-regulation following wine consumption were included. The up-regulation of short-chain fatty acids and the down-regulation of sphingomyelins after wine intake, as well as the up-regulation of gut microbial fermentation metabolites like vanillic and syringic acid are some of the most important findings reported in the reviewed literature. Our results confirm the intact passage of certain wine compounds, such as tartaric acid and other wine acids, to the human organism. In an era where the health effects of wine consumption are of growing interest, this review offers a holistic perspective on the metabolic underpinnings of this centuries-old tradition.
Topics: Humans; Wine; Metabolome; Phenols; Metabolomics; Diet
PubMed: 38005338
DOI: 10.3390/molecules28227616 -
Current Nutrition Reports Sep 2019Metabolomics offers several opportunities for advancement in nutritional cancer epidemiology; however, numerous research gaps and challenges remain. This narrative... (Review)
Review
PURPOSE OF REVIEW
Metabolomics offers several opportunities for advancement in nutritional cancer epidemiology; however, numerous research gaps and challenges remain. This narrative review summarizes current research, challenges, and future directions for epidemiologic studies of nutritional metabolomics and cancer.
RECENT FINDINGS
Although many studies have used metabolomics to investigate either dietary exposures or cancer, few studies have explicitly investigated diet-cancer relationships using metabolomics. Most studies have been relatively small (≤ ~ 250 cases) or have assessed a limited number of nutritional metabolites (e.g., coffee or alcohol-related metabolites). Nutritional metabolomic investigations of cancer face several challenges in study design; biospecimen selection, handling, and processing; diet and metabolite measurement; statistical analyses; and data sharing and synthesis. More metabolomics studies linking dietary exposures to cancer risk, prognosis, and survival are needed, as are biomarker validation studies, longitudinal analyses, and methodological studies. Despite the remaining challenges, metabolomics offers a promising avenue for future dietary cancer research.
Topics: Biomarkers, Tumor; Diet; Epidemiologic Studies; Humans; Metabolome; Metabolomics; Neoplasms; Nutritional Physiological Phenomena; Prognosis
PubMed: 31129888
DOI: 10.1007/s13668-019-00279-z