Metabolomics Tools and Information Retrieval in Microbiome Hacking

Abstract It is increasingly admitted that microbes and the host's biology are tightly linked, and these interactions are crucial for both partners' functional integrity. Thus, interrogating the microbiome allows deciphering its contribution to host health and disease and may enlighten unexplored paths in human pathophysiology. The recent development of powerful technologies, such as metabolomics, enables this exploration through the comprehensive assessment of metabolites to interrogate the microbiome. Metabolomics is an unbiased, data-driven and hypothesis-generating technique that holistically explores biological systems. Nuclear magnetic resonance spectroscopy and mass spectrometry are the main used analytical platforms to retrieve qualitative and quantitative chemical information. This chapter aims to describe major metabolomics technologies and their analytical strengths and limits. Particular focus on microbiome applications will be highlighted when appropriate. Finally, challenges and perspectives of metabolomics will be described.

• Publication year

  2019

• Venue

  Microbiome and Metabolome in Diagnosis, Therapy, and other Strategic Applications

• Publication date

  Unknown publication date

• Fields of study

  Not labeled

• Identifiers
  DOI 10.1016/B978-0-12-815249-2.00005-1
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• A strategy for multimodal data integration: application to biomarkers identification in spinocerebellar ataxia

  2018cited by this paper
• LipidCCS: Prediction of Collision Cross-Section Values for Lipids with High Precision To Support Ion Mobility-Mass Spectrometry-Based Lipidomics.

  2017cited by this paper
• Applications of Mass Spectrometry Imaging to Cancer.

  2017cited by this paper
• Advances in metabolome information retrieval: turning chemistry into biology. Part I: analytical chemistry of the metabolome

  2017cited by this paper
• Sample preparation procedures utilized in microbial metabolomics: An overview.

  2017cited by this paper
• Review of emerging metabolomic tools and resources: 2015–2016

  2017cited by this paper
• Sparse statistical health monitoring: A novel variable selection approach to diagnosis and follow-up of individual patients

  2017cited by this paper
• Capillary electrophoresis mass spectrometry as a tool for untargeted metabolomics.

  2017cited by this paper
• Advances in metabolome information retrieval: turning chemistry into biology. Part II: biological information recovery

  2017cited by this paper
• Recent advances in liquid and gas chromatography methodology for extending coverage of the metabolome.

  2017cited by this paper
• Urinary metabolic phenotyping of mucopolysaccharidosis type I combining untargeted and targeted strategies with data modeling.

  2017cited by this paper
• Direct infusion mass spectrometry for metabolomic phenotyping of diseases.

  2017cited by this paper
• Recent Advances in NMR-Based Metabolomics.

  2017cited by this paper
• Quality assurance and quality control processes: summary of a metabolomics community questionnaire

  2017cited by this paper
• Deep Learning Accurately Predicts Estrogen Receptor Status in Breast Cancer Metabolomics Data

  2017cited by this paper
• A clinician's guide to microbiome analysis

  2017cited by this paper
• Computational Approaches for Integrative Analysis of the Metabolome and Microbiome

  2017cited by this paper
• Collection and Preparation of Clinical Samples for Metabolomics.

  2017cited by this paper
• Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung.

  2017cited by this paper
• Nondestructive tissue analysis for ex vivo and in vivo cancer diagnosis using a handheld mass spectrometry system

  2017cited by this paper
• Network approaches to systems biology analysis of complex disease: integrative methods for multi-omics data

  2017cited by this paper
• Large-Scale Prediction of Collision Cross-Section Values for Metabolites in Ion Mobility-Mass Spectrometry.

  2016cited by this paper
• Clinical Metabolomics: The New Metabolic Window for Inborn Errors of Metabolism Investigations in the Post-Genomic Era

  2016cited by this paper
• Optimization of a liquid chromatography ion mobility-mass spectrometry method for untargeted metabolomics using experimental design and multivariate data analysis.

  2016cited by this paper
• Independent Components Analysis: Theory and Applications

  2016cited by this paper
• Systems-Wide High-Dimensional Data Acquisition and Informatics Using Structural Mass Spectrometry Strategies.

  2016cited by this paper
• Omics-Based Strategies in Precision Medicine: Toward a Paradigm Shift in Inborn Errors of Metabolism Investigations

  2016cited by this paper
• Stable Isotope Resolved Metabolomics Studies in Ex Vivo TIssue Slices.

  2016cited by this paper
• Applications of NMR spectroscopy to systems biochemistry.

  2016cited by this paper
• Molecular Imaging of Growth, Metabolism, and Antibiotic Inhibition in Bacterial Colonies by Laser Ablation Electrospray Ionization Mass Spectrometry.

  2016cited by this paper
• Metabolomics enables precision medicine: “A White Paper, Community Perspective”

  2016cited by this paper
• Normalization and integration of large-scale metabolomics data using support vector regression

  2016cited by this paper
• Sample normalization methods in quantitative metabolomics.

  2016cited by this paper
• Revealing disease-associated pathways by network integration of untargeted metabolomics

  2016cited by this paper
• Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams

  2016cited by this paper
• Comparative assessment of bioanalytical method validation guidelines for pharmaceutical industry.

  2016cited by this paper
• An informatics research agenda to support precision medicine: seven key areas

  2016cited by this paper
• The role of metabolomics in precision medicine

  2016cited by this paper
• A Next Generation Multiscale View of Inborn Errors of Metabolism.

  2016cited by this paper
• MetICA: independent component analysis for high-resolution mass-spectrometry based non-targeted metabolomics

  2016cited by this paper
• Chemometric methods in data processing of mass spectrometry-based metabolomics: A review.

  2016cited by this paper
• Microbiome-metabolome analysis reveals unhealthy alterations in the composition and metabolism of ruminal microbiota with increasing dietary grain in a goat model.

  2016cited by this paper
• Computational Modeling of Human Metabolism and Its Application to Systems Biomedicine.

  2016cited by this paper
• Performance Evaluation and Online Realization of Data-driven Normalization Methods Used in LC/MS based Untargeted Metabolomics Analysis

  2016cited by this paper
• Development and Application of Ultra-Performance Liquid Chromatography-TOF MS for Precision Large Scale Urinary Metabolic Phenotyping.

  2016cited by this paper
• Mass Spectrometry Imaging of Complex Microbial Communities

  2016cited by this paper
• Magnetic resonance spectroscopy — Revisiting the biochemical and molecular milieu of brain tumors

  2016cited by this paper
• Systematic Assessment of Seven Solvent and Solid-Phase Extraction Methods for Metabolomics Analysis of Human Plasma by LC-MS

  2016cited by this paper
• The ecology of the microbiome: Networks, competition, and stability

  2015cited by this paper
• Systems biology of host–microbe metabolomics

  2015cited by this paper
• Using prior knowledge from cellular pathways and molecular networks for diagnostic specimen classification

  2015cited by this paper
• Validation of chemometric models - a tutorial.

  2015cited by this paper
• Systems Biology of the Fluxome

  2015cited by this paper
• MetaboAnalyst 3.0—making metabolomics more meaningful

  2015cited by this paper
• Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires

  2015cited by this paper
• An integrated targeted metabolomic platform for high-throughput metabolite profiling and automated data processing

  2015cited by this paper
• Personalized Nutrition by Prediction of Glycemic Responses.

  2015cited by this paper
• Analytical Methods in Untargeted Metabolomics: State of the Art in 2015

  2015cited by this paper
• Methods of integrating data to uncover genotype–phenotype interactions

  2015cited by this paper
• The Relationship Between Trimethylamine-N-Oxide and Prevalent Cardiovascular Disease in a Multiethnic Population Living in Canada.

  2015cited by this paper
• Library preparation methodology can influence genomic and functional predictions in human microbiome research

  2015cited by this paper
• Molecular cartography of the human skin surface in 3D

  2015cited by this paper
• Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis.

  2015cited by this paper
• 164 Gut Microbiome Biomarkers Are Associated With Clinical Response to a Low FODMAP Diet in Children With Irritable Bowel Syndrome

  2015cited by this paper
• Extraction parameters for metabolomics from cultured cells.

  2015cited by this paper
• From metabolomics to fluxomics: a computational procedure to translate metabolite profiles into metabolic fluxes.

  2015cited by this paper
• Ion Mobility-Derived Collision Cross Section As an Additional Measure for Lipid Fingerprinting and Identification

  2014cited by this paper
• Computational Strategies for a System-Level Understanding of Metabolism

  2014cited by this paper
• Towards the Disease Biomarker in an Individual Patient Using Statistical Health Monitoring

  2014cited by this paper
• Relating the metatranscriptome and metagenome of the human gut

  2014cited by this paper
• A short history of chemometrics: a personal view

  2014cited by this paper
• Current breathomics—a review on data pre-processing techniques and machine learning in metabolomics breath analysis

  2014cited by this paper
• Role of Cationization and Multimers Formation for Diastereomers Differentiation by Ion Mobility-Mass Spectrometry

  2013cited by this paper
• NMR-based metabolomics in human disease diagnosis: applications, limitations, and recommendations

  2013cited by this paper
• Intraoperative Tissue Identification Using Rapid Evaporative Ionization Mass Spectrometry

  2013cited by this paper
• New advances in separation science for metabolomics: resolving chemical diversity in a post-genomic era.

  2013cited by this paper
• Fluxomics - connecting 'omics analysis and phenotypes.

  2013cited by this paper
• Liquid chromatography-mass spectrometry in metabolomics research: mass analyzers in ultra high pressure liquid chromatography coupling.

  2013cited by this paper
• Predicting Network Activity from High Throughput Metabolomics

  2013cited by this paper
• Guest editorial. Computational systems biology.

  2013cited by this paper
• A metabolomic view of how the human gut microbiota impacts the host metabolome using humanized and gnotobiotic mice

  2013cited by this paper
• Molecular analysis of model gut microbiotas by imaging mass spectrometry and nanodesorption electrospray ionization reveals dietary metabolite transformations.

  2012cited by this paper
• Stitching together Multiple Data Dimensions Reveals Interacting Metabolomic and Transcriptomic Networks That Modulate Cell Regulation

  2012cited by this paper
• The importance of experimental design and QC samples in large-scale and MS-driven untargeted metabolomic studies of humans.

  2012cited by this paper
• Current trends and challenges in sample preparation for global metabolomics using liquid chromatography–mass spectrometry

  2012cited by this paper
• Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

  2011cited by this paper
• Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data

  2011cited by this paper
• The Roots of Bioinformatics in Theoretical Biology

  2011cited by this paper
• Network medicine: a network-based approach to human disease

  2010cited by this paper
• Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism

  2009cited by this paper
• Metabolomics Reveals Metabolic Biomarkers of Crohn's Disease

  2009cited by this paper
• Biomolecular structural separations by ion mobility–mass spectrometry

  2008cited by this paper
• Metabolomics and fluxomics approaches.

  2008cited by this paper
• Proposed minimum reporting standards for chemical analysis

  2007cited by this paper
• UvA-DARE ( Digital Academic Repository ) Centering , scaling and transformations : improving the biological information content of metabolomics data

  2006cited by this paper
• Metabolomics – the link between genotypes and phenotypes

  2004cited by this paper
• Systems Biology: A Brief Overview

  2002cited by this paper
• 'Metabonomics': understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data.

  1999cited by this paper
• Systematic functional analysis of the yeast genome.

  1998cited by this paper
• Quantitative analysis of urine vapor and breath by gas-liquid partition chromatography.

  1971cited by this paper

• No citing papers are available for this paper.