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Nature Reviews. Microbiology Mar 2022Microbiotas are a malleable part of ecosystems, including the human ecosystem. Microorganisms affect not only the chemistry of their specific niche, such as the human... (Review)
Review
Microbiotas are a malleable part of ecosystems, including the human ecosystem. Microorganisms affect not only the chemistry of their specific niche, such as the human gut, but also the chemistry of distant environments, such as other parts of the body. Mass spectrometry-based metabolomics is one of the key technologies to detect and identify the small molecules produced by the human microbiota, and to understand the functional role of these microbial metabolites. This Review provides a foundational introduction to common forms of untargeted mass spectrometry and the types of data that can be obtained in the context of microbiome analysis. Data analysis remains an obstacle; therefore, the emphasis is placed on data analysis approaches and integrative analysis, including the integration of microbiome sequencing data.
Topics: Animals; Humans; Mass Spectrometry; Metabolome; Metabolomics; Microbiota
PubMed: 34552265
DOI: 10.1038/s41579-021-00621-9 -
Trends in Biotechnology Nov 2022Owing to recent advances in mass spectrometry (MS), tens to hundreds of proteins, lipids, and small molecules can be measured in single cells. The ability to... (Review)
Review
Owing to recent advances in mass spectrometry (MS), tens to hundreds of proteins, lipids, and small molecules can be measured in single cells. The ability to characterize the molecular heterogeneity of individual cells is necessary to define the full assortment of cell subtypes and identify their function. We review single-cell MS including high-throughput, targeted, mass cytometry-based approaches and antibody-free methods for broad profiling of the proteome and metabolome of single cells. The advantages and disadvantages of different methods are discussed, as well as the challenges and opportunities for further improvements in single-cell MS. These methods is being used in biomedicine in several applications including revealing tumor heterogeneity and high-content drug screening.
Topics: Lipids; Mass Spectrometry; Metabolome; Metabolomics; Proteome
PubMed: 35562238
DOI: 10.1016/j.tibtech.2022.04.004 -
Journal of Genetics and Genomics = Yi... Feb 2020Mass spectrometry (MS)-based omics technologies are now widely used to profile small molecules in multiple matrices to confer comprehensive snapshots of cellular... (Review)
Review
Mass spectrometry (MS)-based omics technologies are now widely used to profile small molecules in multiple matrices to confer comprehensive snapshots of cellular metabolic phenotypes. The metabolomes of cells, tissues, and organisms comprise a variety of molecules including lipids, amino acids, sugars, organic acids, and so on. Metabolomics mainly focus on the hydrophilic classes, while lipidomics has emerged as an independent omics owing to the complexities of the organismal lipidomes. The potential roles of lipids and small metabolites in disease pathogenesis have been widely investigated in various human diseases, but system-level understanding is largely lacking, which could be partly attributed to the insufficiency in terms of metabolite coverage and quantitation accuracy in current analytical technologies. While scientists are continuously striving to develop high-coverage omics approaches, integration of metabolomics and lipidomics is becoming an emerging approach to mechanistic investigation. Integration of metabolome and lipidome offers a complete atlas of the metabolic landscape, enabling comprehensive network analysis to identify critical metabolic drivers in disease pathology, facilitating the study of interconnection between lipids and other metabolites in disease progression. In this review, we summarize omics-based findings on the roles of lipids and metabolites in the pathogenesis of selected major diseases threatening public health. We also discuss the advantages of integrating lipidomics and metabolomics for in-depth understanding of molecular mechanism in disease pathogenesis.
Topics: Disease Progression; Humans; Lipid Metabolism; Lipidomics; Lipids; Mass Spectrometry; Metabolome; Metabolomics
PubMed: 32178981
DOI: 10.1016/j.jgg.2019.11.009 -
Signal Transduction and Targeted Therapy Mar 2023Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite accumulation or deficiency which is well-recognized hallmarks of diseases.... (Review)
Review
Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite accumulation or deficiency which is well-recognized hallmarks of diseases. Metabolite signatures that have close proximity to subject's phenotypic informative dimension, are useful for predicting diagnosis and prognosis of diseases as well as monitoring treatments. The lack of early biomarkers could lead to poor diagnosis and serious outcomes. Therefore, noninvasive diagnosis and monitoring methods with high specificity and selectivity are desperately needed. Small molecule metabolites-based metabolomics has become a specialized tool for metabolic biomarker and pathway analysis, for revealing possible mechanisms of human various diseases and deciphering therapeutic potentials. It could help identify functional biomarkers related to phenotypic variation and delineate biochemical pathways changes as early indicators of pathological dysfunction and damage prior to disease development. Recently, scientists have established a large number of metabolic profiles to reveal the underlying mechanisms and metabolic networks for therapeutic target exploration in biomedicine. This review summarized the metabolic analysis on the potential value of small-molecule candidate metabolites as biomarkers with clinical events, which may lead to better diagnosis, prognosis, drug screening and treatment. We also discuss challenges that need to be addressed to fuel the next wave of breakthroughs.
Topics: Humans; Biomarkers; Metabolomics; Metabolome; Metabolic Networks and Pathways
PubMed: 36941259
DOI: 10.1038/s41392-023-01399-3 -
Nucleic Acids Research Jan 2022The Human Metabolome Database or HMDB (https://hmdb.ca) has been providing comprehensive reference information about human metabolites and their associated biological,...
The Human Metabolome Database or HMDB (https://hmdb.ca) has been providing comprehensive reference information about human metabolites and their associated biological, physiological and chemical properties since 2007. Over the past 15 years, the HMDB has grown and evolved significantly to meet the needs of the metabolomics community and respond to continuing changes in internet and computing technology. This year's update, HMDB 5.0, brings a number of important improvements and upgrades to the database. These should make the HMDB more useful and more appealing to a larger cross-section of users. In particular, these improvements include: (i) a significant increase in the number of metabolite entries (from 114 100 to 217 920 compounds); (ii) enhancements to the quality and depth of metabolite descriptions; (iii) the addition of new structure, spectral and pathway visualization tools; (iv) the inclusion of many new and much more accurately predicted spectral data sets, including predicted NMR spectra, more accurately predicted MS spectra, predicted retention indices and predicted collision cross section data and (v) enhancements to the HMDB's search functions to facilitate better compound identification. Many other minor improvements and updates to the content, the interface, and general performance of the HMDB website have also been made. Overall, we believe these upgrades and updates should greatly enhance the HMDB's ease of use and its potential applications not only in human metabolomics but also in exposomics, lipidomics, nutritional science, biochemistry and clinical chemistry.
Topics: Databases, Genetic; Humans; Lipidomics; Mass Spectrometry; Metabolome; Metabolomics; User-Computer Interface
PubMed: 34986597
DOI: 10.1093/nar/gkab1062 -
Sports Medicine (Auckland, N.Z.) Mar 2022Metabolomics is a field of omics science that involves the comprehensive measurement of small metabolites in biological samples. It is increasingly being used to study...
BACKGROUND
Metabolomics is a field of omics science that involves the comprehensive measurement of small metabolites in biological samples. It is increasingly being used to study exercise physiology and exercise-associated metabolism. However, the field of exercise metabolomics has not been extensively reviewed or assessed.
OBJECTIVE
This review on exercise metabolomics has three aims: (1) to provide an introduction to the general workflow and the different metabolomics technologies used to conduct exercise metabolomics studies; (2) to provide a systematic overview of published exercise metabolomics studies and their findings; and (3) to discuss future perspectives in the field of exercise metabolomics.
METHODS
We searched electronic databases including Google Scholar, Science Direct, PubMed, Scopus, Web of Science, and the SpringerLink academic journal database between January 1st 2000 and September 30th 2020.
RESULTS
Based on our detailed analysis of the field, exercise metabolomics studies fall into five major categories: (1) exercise nutrition metabolism; (2) exercise metabolism; (3) sport metabolism; (4) clinical exercise metabolism; and (5) metabolome comparisons. Exercise metabolism is the most popular category. The most common biological samples used in exercise metabolomics studies are blood and urine. Only a small minority of exercise metabolomics studies employ targeted or quantitative techniques, while most studies used untargeted metabolomics techniques. In addition, mass spectrometry was the most commonly used platform in exercise metabolomics studies, identified in approximately 54% of all published studies. Our data indicate that biomarkers or biomarker panels were identified in 34% of published exercise metabolomics studies.
CONCLUSION
Overall, there is an increasing trend towards better designed, more clinical, mass spectrometry-based metabolomics studies involving larger numbers of participants/patients and larger numbers of metabolites being identified.
Topics: Biomarkers; Exercise; Humans; Metabolome; Metabolomics; Sports
PubMed: 34716906
DOI: 10.1007/s40279-021-01582-y -
Small Methods Jul 2022Mass spectrometry-based metabolomics has emerged as a powerful technique for biomedical research, although technical issues with its analytical precision and structural...
Mass spectrometry-based metabolomics has emerged as a powerful technique for biomedical research, although technical issues with its analytical precision and structural characterization remain. Herein, a robust non-targeted strategy for accurate quantitation and precise profiling of metabolomes is developed and applied to investigate plasma metabolic features associated with human aging. A comprehensive set of isotope-labeled standards (ISs) covering major metabolic pathways is incorporated to quantify polar metabolites. Matching rules to select ISs for calibration follow a primary criterion of minimal coefficients of variations (COVs). If minimal COVs between specific ISs for a particular metabolite fall within 5% window, a further selection of ISs is conducted based on structural similarities and proximity in retention time. The introduction and refined selection of appropriate ISs for quantitation reduces the COVs of 480 identified metabolites in quality control samples from 14.3% to 9.8% and facilitates identification of additional metabolite. Finally, the precise metabolomics approach reveals perturbations in a diverse array of metabolic pathways across aging that principally implicate steroid metabolism, amino acid metabolism, lipid metabolism, and purine metabolism, which allows the authors to draw correlates to the pathology of various age-related diseases. These findings provide clues for the prevention and treatment of these age-related diseases.
Topics: Aging; Humans; Mass Spectrometry; Metabolic Networks and Pathways; Metabolome; Metabolomics
PubMed: 35527334
DOI: 10.1002/smtd.202200130 -
Cell Jun 2020Metabolism during pregnancy is a dynamic and precisely programmed process, the failure of which can bring devastating consequences to the mother and fetus. To define a...
Metabolism during pregnancy is a dynamic and precisely programmed process, the failure of which can bring devastating consequences to the mother and fetus. To define a high-resolution temporal profile of metabolites during healthy pregnancy, we analyzed the untargeted metabolome of 784 weekly blood samples from 30 pregnant women. Broad changes and a highly choreographed profile were revealed: 4,995 metabolic features (of 9,651 total), 460 annotated compounds (of 687 total), and 34 human metabolic pathways (of 48 total) were significantly changed during pregnancy. Using linear models, we built a metabolic clock with five metabolites that time gestational age in high accordance with ultrasound (R = 0.92). Furthermore, two to three metabolites can identify when labor occurs (time to delivery within two, four, and eight weeks, AUROC ≥ 0.85). Our study represents a weekly characterization of the human pregnancy metabolome, providing a high-resolution landscape for understanding pregnancy with potential clinical utilities.
Topics: Adult; Biomarkers; Female; Fetus; Gestational Age; Humans; Metabolic Networks and Pathways; Metabolome; Metabolomics; Pregnancy; Pregnant Women
PubMed: 32589958
DOI: 10.1016/j.cell.2020.05.002 -
Nutrients May 2023Obesity is a disorder identified by an inappropriate increase in weight in relation to height and is considered by many international health institutions to be a major... (Review)
Review
Obesity is a disorder identified by an inappropriate increase in weight in relation to height and is considered by many international health institutions to be a major pandemic of the 21st century. The gut microbial ecosystem impacts obesity in multiple ways that yield downstream metabolic consequences, such as affecting systemic inflammation, immune response, and energy harvest, but also the gut-host interface. Metabolomics, a systematized study of low-molecular-weight molecules that take part in metabolic pathways, represents a serviceable method for elucidation of the crosstalk between hosts' metabolism and gut microbiota. In the present review, we confer about clinical and preclinical studies exploring the association of obesity and related metabolic disorders with various gut microbiome profiles, and the effects of several dietary interventions on gut microbiome composition and the metabolome. It is well established that various nutritional interventions may serve as an efficient therapeutic approach to support weight loss in obese individuals, yet no agreement exists in regard to the most effective dietary protocol, both in the short and long term. However, metabolite profiling and the gut microbiota composition might represent an opportunity to methodically establish predictors for obesity control that are relatively simple to measure in comparison to traditional approaches, and it may also present a tool to determine the optimal nutritional intervention to ameliorate obesity in an individual. Nevertheless, a lack of adequately powered randomized trials impedes the application of observations to clinical practice.
Topics: Humans; Gastrointestinal Microbiome; Ecosystem; Obesity; Metabolome; Metabolomics
PubMed: 37242119
DOI: 10.3390/nu15102236 -
Phytochemical Analysis : PCA Mar 2020Metabolomics is a fast growing technology that has effectively contributed to many plant-related sciences and drug discovery.
INTRODUCTION
Metabolomics is a fast growing technology that has effectively contributed to many plant-related sciences and drug discovery.
OBJECTIVE
To use the non-targeted metabolomics approach to investigate the chemical profiles of three Malvaceae plants, namely Hibiscus mutabilis L. (Changing rose), H. schizopetalus (Dyer) Hook.f. (Coral Hibiscus), and Malvaviscus arboreus Cav. (Sleeping Hibiscus), along with evaluating their antioxidant and anti-infective potential.
METHODOLOGY
Metabolic profiling was carried out using liquid chromatography coupled with high-resolution electrospray ionisation mass spectrometry (LC-HR-ESI-MS) for dereplication purposes. The chemical composition of the studied plants was further compared by principal component analysis (PCA). The antioxidant and anti-infective properties of their different extracts were correlated to their phytochemical profiles by orthogonal partial least square discriminant analysis (OPLS-DA).
RESULTS
A variety of structurally different metabolites, mostly phenolics, were characterized. Comparing the distribution pattern of these tentatively identified metabolites among the studied plant species/fractions revealed the chemical uniqueness of the dichloromethane fraction of M. arboreus. Some extracts and fractions of these plants demonstrated noteworthy antioxidant and antitrypanosomal potential; the latter was partly attributed to their anti-protease activities. The active principles of these plants were pinpointed before any laborious isolation steps, to avoid the redundant isolation of previously known compounds.
CONCLUSION
This study highlighted the use of the established procedure in exploring the metabolomes of these species, which could be helpful for chemotaxonomic and authentication purposes, and might expand the basis for their future phytochemical analysis. Coupling the observed biological potential with LC-MS data has also accelerated the tracing of their bioactive principles.
Topics: Chromatography, High Pressure Liquid; Malvaceae; Metabolome; Metabolomics; Phytochemicals; Plant Extracts; Spectrometry, Mass, Electrospray Ionization
PubMed: 31390115
DOI: 10.1002/pca.2883