Microbial Metabolomics

Microbial metabolomics constitutes an integrated component of systems biology. By studying the complete set of metabolites within a microorganism and monitoring the global outcome of interactions between its development processes and the environment, metabolomics can potentially provide a more accurate snap shot of the actual physiological state of the cell. Recent advancement of technologies and post-genomic developments enable the study and analysis of metabolome. This unique contribution resulted in many scientific disciplines incorporating metabolomics as one of their “omics” platforms. This review focuses on metabolomics in microorganisms and utilizes selected topics to illustrate its impact on the understanding of systems microbiology.

• Publication year

  2011

• Venue

  Current Genomics

• Publication date

  2011-09-01

• Fields of study

  Biology, Medicine, Chemistry, Environmental Science

• Identifiers
  DOI 10.2174/138920211797248619PMID 22379393PMCID 3178908
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Unravelling the effects of the environment and host genotype on the gut microbiome

  2011influential reference
• Lessons from Genomics

  2011cited by this paper
• Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species

  2011influential reference
• The Gut's Clostridium Cocktail

  2011cited by this paper
• A Persistent Oxygen Anomaly Reveals the Fate of Spilled Methane in the Deep Gulf of Mexico

  2011cited by this paper
• A Systems Biology Approach to Infectious Disease Research: Innovating the Pathogen-Host Research Paradigm

  2011cited by this paper
• Shifting the balance: antibiotic effects on host–microbiota mutualism

  2011influential reference
• The Human Genome at 10: Successes and Challenges

  2011cited by this paper
• The skin microbiome

  2011cited by this paper
• Microbiology. Going viral: exploring the role of viruses in our bodies.

  2011cited by this paper
• Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria

  2010cited by this paper
• A human gut microbial gene catalogue established by metagenomic sequencing

  2010cited by this paper
• Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

  2010cited by this paper
• A glut from the gut: metagenomics takes a giant step foward

  2010cited by this paper
• Comparative Analyses of the Bacterial Microbiota of the Human Nostril and Oropharynx

  2010cited by this paper
• Metabolome-Proteome Differentiation Coupled to Microbial Divergence

  2010influential reference
• Body's hardworking microbes get some overdue respect.

  2010cited by this paper
• Genomic encyclopedia of sugar utilization pathways in the Shewanella genus

  2010cited by this paper
• Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean

  2010cited by this paper
• A survey of current software for network analysis in molecular biology

  2010cited by this paper
• Longitudinal shift in diabetic wound microbiota correlates with prolonged skin defense response

  2010cited by this paper
• BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

  2010influential reference
• Carbon metabolism of intracellular bacterial pathogens and possible links to virulence

  2010cited by this paper
• Clinical Applications of Metabolomics in Oncology: A Review

  2009influential reference
• Is there a future for probiotics in preventing Clostridium difficile-associated disease and treatment of recurrent episodes?

  2009cited by this paper
• A systems biology approach to the identification and analysis of transcriptional regulatory networks in osteocytes

  2009influential reference
• Unraveling mechanisms of action of probiotics.

  2009cited by this paper
• Systems Biology: Functional analysis of natural microbial consortia using community proteomics

  2009influential reference
• Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream

  2009influential reference
• Microbiome Metagenomic Analysis of the Human Distal Gut

  2009influential reference
• Genome-scale analyses of health-promoting bacteria: probiogenomics

  2009influential reference
• TerraGenome: a consortium for the sequencing of a soil metagenome

  2009cited by this paper
• Topographical and Temporal Diversity of the Human Skin Microbiome

  2009cited by this paper
• The use of probiotics in the prevention and treatment of antibiotic-associated diarrhea with special interest in Clostridium difficile-associated diarrhea.

  2009cited by this paper
• Reconstruction of biochemical networks in microorganisms

  2009influential reference
• The NIH Human Microbiome Project.

  2009cited by this paper
• The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

  2009influential reference
• Systems biology: Metabonomics

  2008cited by this paper
• Symbiotic gut microbes modulate human metabolic phenotypes

  2008cited by this paper
• Worlds within worlds: evolution of the vertebrate gut microbiota

  2008cited by this paper
• Separation and mass spectrometry in microbial metabolomics.

  2008influential reference
• Noninvasive metabolomic profiling of embryo culture media using proton nuclear magnetic resonance correlates with reproductive potential of embryos in women undergoing in vitro fertilization.

  2008cited by this paper
• Genome-scale models of bacterial metabolism: reconstruction and applications

  2008influential reference
• Molecular eco-systems biology: towards an understanding of community function

  2008influential reference
• New surveyor tools for charting microbial metabolic maps

  2008influential reference
• Depiction of metabolome changes in histidine-starved Escherichia coli by CE-TOFMS.

  2008cited by this paper
• HMDB: a knowledgebase for the human metabolome

  2008cited by this paper
• The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects.

  2007cited by this paper
• Get the most out of your metagenome: computational analysis of environmental sequence data.

  2007cited by this paper
• The Metabolomics Standards Initiative

  2007cited by this paper
• The Human Microbiome Project

  2007cited by this paper
• Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time

  2007cited by this paper
• The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific

  2007cited by this paper
• Diet and the evolution of human amylase gene copy number variation

  2007cited by this paper
• Pathogen profiling for disease management and surveillance

  2007cited by this paper
• Microbial ecology: Human gut microbes associated with obesity

  2006influential reference
• Communication in bacteria: an ecological and evolutionary perspective

  2006influential reference
• Metabolomics: Current technologies and future trends

  2006cited by this paper
• Bacterially speaking.

  2006cited by this paper
• Cooperation among Microorganisms

  2006cited by this paper
• Metagenomic Analysis of the Human Distal Gut Microbiome

  2006cited by this paper
• An obesity-associated gut microbiome with increased capacity for energy harvest

  2006cited by this paper
• Metabolic Engineering in the -omics Era: Elucidating and Modulating Regulatory Networks

  2005cited by this paper
• Application of MALDI-TOF mass spectrometry in screening and diagnostic research.

  2005cited by this paper
• Genomic studies of uncultivated archaea

  2005influential reference
• Metagenomics: DNA sequencing of environmental samples

  2005cited by this paper
• The Consortium for Metabonomic Toxicology (COMET): aims, activities and achievements.

  2005cited by this paper
• Measuring the metabolome: current analytical technologies.

  2005cited by this paper
• Discrimination of pathogenic clinical isolates and laboratory strains of Bacillus cereus by NMR-based metabolomic profiling.

  2005cited by this paper
• METLIN: A Metabolite Mass Spectral Database

  2005cited by this paper
• Metabolomics reviewed: a new "omics" platform technology for systems biology and implications for natural products research.

  2005influential reference
• Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach

  2005cited by this paper
• Gut microorganisms, mammalian metabolism and personalized health care

  2005influential reference
• Mass spectrometry in metabolome analysis.

  2005influential reference
• The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533.

  2004cited by this paper
• Community structure and metabolism through reconstruction of microbial genomes from the environment

  2004cited by this paper
• Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota.

  2004cited by this paper
• Comparative Metagenomics of Microbial Communities

  2004influential reference
• Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network.

  2003cited by this paper
• Chemical diagnosis of Lesch-Nyhan syndrome using gas chromatography-mass spectrometry detection.

  2003cited by this paper
• Monitoring changes in anthocyanin and steroid alkaloid glycoside content in lines of transgenic potato plants using liquid chromatography/mass spectrometry.

  2003cited by this paper
• Identification and quantification of carotenoids, tocopherols and chlorophylls in commonly consumed fruits and vegetables.

  2003cited by this paper
• Metabolic networks of Cucurbita maxima phloem.

  2003cited by this paper
• Taxus metabolomics: methyl jasmonate preferentially induces production of taxoids oxygenated at C-13 in Taxus x media cell cultures.

  2003cited by this paper
• The role of chemical fingerprinting: application to Ephedra.

  2003cited by this paper
• Gene-culture coevolution between cattle milk protein genes and human lactase genes

  2003cited by this paper
• Microbial diversity and function in soil: from genes to ecosystems.

  2002cited by this paper
• Rapid and noninvasive diagnosis of the presence and severity of coronary heart disease using 1H-NMR-based metabonomics

  2002cited by this paper
• Abnormal colonic fermentation in irritable bowel syndrome.

  1998cited by this paper
• Prokaryotes: the unseen majority.

  1998cited by this paper
• Epithelial cell growth and differentiation. III. Promoting diversity in the intestine: conversations between the microflora, epithelium, and diffuse GALT.

  1997cited by this paper
• Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.

  1995cited by this paper
• International Journal of Research and Development in Pharmacy and Life Sciences Metabolomics: Current Technologies and Future Trends

  year unknowninfluential reference

• Gut ecosystem dysfunction in parkinson's disease: deciphering faecal metabolome-metagenome links for novel diagnostic panels.

  2026cites this paper
• A chemically informed framework for microbial consortia analysis beyond sequences: A narrative review

  2025cites this paper
• Exploring the Causal Relationship Between Blood Metabolites and Chronic Periodontitis: Insights From Genetic Causal Analysis

  2025cites this paper
• Metabolic fingerprinting to elucidate the biodegradation of phosphonoacetic acid and its impact on Penicillium metabolism

  2025cites this paper
• Influence of dietary components on the gut microbiota of middle-aged adults: the gut-Mediterranean connection

  2025cites this paper
• Qualitative and Quantitative Metabolite Comparison of Grain, Persimmon, and Apple Vinegars with Antioxidant Activities

  2025cites this paper
• Meta-analysis of probiotics metabolites in gastrointestinal tract and metabolic health

  2025cites this paper
• Untargeted analysis of hydrophilic metabolites using enhanced LC-MS separation with a pentafluoro phenylpropyl-functionalized column and prediction-based MS/MS spectrum annotation

  2025cites this paper
• Gut Microbiome Interventions: From Dysbiosis to Next-Generation Probiotics (NGPs) for Disease Management

  2025cites this paper
• Multiomics Provides a New Understanding of the Effect of Temperature Change on the Fermentation Quality of Ophiocordyceps sinensis

  2025cites this paper
• Biochemical and chemical markers associated with biodeterioration agents isolated from archive audio-visual materials

  2025cites this paper
• Recent advances in yeast and bacteria co-cultivation for bioprocess applications

  2025cites this paper
• Research Progress of Metabonomics in Traumatic Brain Injury

  2024cites this paper
• Multi-Omics Analysis Unravels the Impact of Stool Sample Logistics on Metabolites and Microbial Composition

  2024cites this paper
• A Comprehensive Overview of Postbiotics with a Special Focus on Discovery Techniques and Clinical Applications

  2024cites this paper
• Beyond the Gut: The intratumoral microbiome's influence on tumorigenesis and treatment response

  2024cites this paper
• Bacterial metabolomics: current applications for human welfare and future aspects

  2024cites this paper
• Designing Primer-Probe Sets for Escherichia coli and E. coli O157 Detection: Comparative Genomic Approach and Food Interference Assessment

  2024cites this paper
• Breaking boundaries in microbiology: customizable nanoparticles transforming microbial detection.

  2024cites this paper
• Unveiling the regulatory mechanism of poly-γ-glutamic acid on soil characteristics under drought stress through integrated metagenomics and metabolomics analysis

  2024cites this paper
• Biobased short chain fatty acid production - Exploring microbial community dynamics and metabolic networks through kinetic and microbial modeling approaches.

  2024cites this paper
• Recent advances in plant translational genomics for crop improvement.

  2024cites this paper
• Metabolomic Differences between Viable but Nonculturable and Recovered Lacticaseibacillus paracasei Zhang

  2023cites this paper
• Unveiling the Gut Microbiome: How Junk Food Impacts the Gut

  2023cites this paper
• Study of chemical constituents, antioxidants and antimicrobial activities of Tamarindus indica L. seed.

  2023cites this paper
• Modulators of a robust and efficient metabolism: Perspective and insights from the Rid superfamily of proteins.

  2023cites this paper
• Intelligent Biological Networks: Improving Anti-Microbial Resistance Resilience through Nutritional Interventions to Understand Protozoal Gut Infections

  2023cites this paper
• 基于气相色谱-质谱法的广泛靶向代谢组学方法开发

  2023cites this paper
• New Approach for the Identification of Isobaric and Isomeric Metabolites

  2023cites this paper
• Comparison of freeze-thaw and sonication cycle-based methods for extracting AMR-associated metabolites from Staphylococcus aureus

  2023cites this paper
• Microbiota shaping and bioburden monitoring of indoor antimicrobial surfaces

  2023cites this paper
• Current Limitations of Staph Infection Diagnostics, and the Role for VOCs in Achieving Culture-Independent Detection

  2023cites this paper
• Contribution of −Omics Technologies in the Study of Porphyromonas gingivalis during Periodontitis Pathogenesis: A Minireview

  2022cites this paper
• Early intraabdominal complications after laparoscopic appendectomy: the status quo and the prospects for prevention

  2022cites this paper
• Application of Metabolomics in Fungal Research

  2022cites this paper
• Metabolomic insight into the synergistic mechanism of action of a bacterial consortium in plant growth promotion.

  2022cites this paper
• Metabolomics-Driven Exploration of the Antibacterial Activity and Mechanism of 2-Methoxycinnamaldehyde

  2022cites this paper
• Apex Predator Nematodes and Meso-Predator Bacteria Consume Their Basal Insect Prey through Discrete Stages of Chemical Transformations

  2022cites this paper
• Exometabolomic analysis of susceptible and multi‐drug resistant Pseudomonas aeruginosa

  2022cites this paper
• Bacterial Metabolomics: Sample Preparation Methods

  2022cites this paper
• Hyperglycemia and cancer in human lung carcinoma by means of Raman spectroscopy and imaging

  2022cites this paper
• Niche adaptation of Frankia do not drastically influence their metabolic profiling

  2022cites this paper
• Treatment Technology of Microbial Landscape Aquatic Plants for Water Pollution

  2021cites this paper
• The oral microbiome: Role of key organisms and complex networks in oral health and disease

  2021cites this paper
• Microbial community diversity in a wastewater treatment plant

  2021cites this paper
• Using metabolomics to guide strategies to tackle the issue of the contamination of food and feed with mycotoxins: A review of the literature with specific focus on Fusarium mycotoxins

  2021cites this paper
• Identification of bacteria in the tracheal swabs of farmed ostriches and their effect on the viability of influenza A virus

  2021cites this paper
• Influence of Supplementation of Lactoferrin, Melittin and Cecropin A to Rat Diet on Changes in Faecal Ammonia Concentrations, Short-Chain Fatty Acid Concentrations and Activities of Bacterial Enzymes

  2021cites this paper
• Infrared MALDI Mass Spectrometry with Laser-Induced Postionization for Imaging of Bacterial Colonies.

  2021cites this paper
• Reflections on the Use of an Invertebrate Chordate Model System for Studies of Gut Microbial Immune Interactions

  2021cites this paper
• Omics-Driven Biotechnology for Industrial Applications

  2021cites this paper
• Metabolomic analysis of Trichophyton rubrum and Microsporum canis during keratin degradation

  2021cites this paper
• Microbiota as Drivers and as Therapeutic Targets in Ocular and Tissue Specific Autoimmunity

  2021cites this paper
• Chemical ecology of a tripartite symbiosis 1

  2021cites this paper
• Metagenomic Characterization of The Tracheobronchial Microbiome in Lung Cancer

  2021cites this paper
• Synergistic antibacterial combination of Sapindoside A and B changes the fatty acid compositions and membrane properties of Cutibacterium acnes.

  2021cites this paper
• Different Wines from Different Yeasts? “Saccharomyces cerevisiae Intraspecies Differentiation by Metabolomic Signature and Sensory Patterns in Wine”

  2021cites this paper
• Effect of cultivation media and temperature on metabolite profiles of three nematicidal Bacillus species

  2021cites this paper
• Metabolomics of Infectious Disease

  2021cites this paper
• Toxicometabolomics: Small Molecules to Answer Big Toxicological Questions

  2021cites this paper
• Metabolomics Comparison of Drug-Resistant and Drug-Susceptible Pseudomonas aeruginosa Strain (Intra- and Extracellular Analysis)

  2021cites this paper
• Interaction Networks in Microbiome Studies

  2021cites this paper
• Metabolomics Data Treatment: Basic Directions of the Full Process.

  2021cites this paper
• Network analyses in microbiome based on high-throughput multi-omics data

  2020cites this paper
• FUNCTIONAL METABOLOMICS DECIPHER BIOCHEMICAL FUNCTIONS AND ASSOCIATED MECHANISMS UNDERLIE SMALL-MOLECULE METABOLISM.

  2020cites this paper
• Intracellular metabolite profiling and the evaluation of metabolite extraction solvents for Clostridium carboxidivorans fermenting carbon monoxide

  2020cites this paper
• Implementation of liquid chromatography-high resolution mass spectrometry methods for untargeted metabolomic analyses of biological samples: A tutorial.

  2020cites this paper
• Microbiological Advancements for Higher Altitude Agro-Ecosystems & Sustainability

  2020cites this paper
• Antimicrobial Resistance in Veterinary Medicine: An Overview

  2020cites this paper
• Use of untargeted metabolomics for assessing soil quality and microbial function

  2020influential citation
• Linoleic acid induces metabolic stress in the intestinal microorganism Bifidobacterium breve DSM 20213

  2020cites this paper
• Applications of Advanced Omics Technology for Harnessing the High Altitude Agriculture Production

  2020cites this paper
• Metabolomics Analysis Reveals Global Metabolic Changes in the Evolved E. coli Strain with Improved Growth and 1-Butanol Production in Minimal Medium

  2020cites this paper
• In vitro human colonic microbiota utilises D-β-hydroxybutyrate to increase butyrogenesis

  2020cites this paper
• Gut–Brain Axis and Neurodegeneration: State-of-the-Art of Meta-Omics Sciences for Microbiota Characterization

  2020cites this paper
• Connecting the dots: Advances in modern metabolomics and its application in yeast system.

  2020cites this paper
• Towards continuous industrial bioprocessing with solventogenic and acetogenic clostridia: challenges, progress and perspectives

  2020cites this paper
• Techniques and methods of microbiomics and their applications

  2020cites this paper
• Chemical Communication in Songbirds

  2020cites this paper
• Effect of diet and intestinal AhR expression on fecal microbiome and metabolomic profiles

  2020cites this paper
• Omics Tools: Approaches for Microbiomes Analysis to Enhance Bioenergy Production

  2020cites this paper
• A multidimensional perspective on microbial interactions

  2019cites this paper
• NMR-Metabolomics Shows That BolA Is an Important Modulator of Salmonella Typhimurium Metabolic Processes under Virulence Conditions

  2019cites this paper
• Metabolite profiling of Bacillus species with nematicidal activity

  2019influential citation
• Bioassay- and metabolomics-guided screening of bioactive soil actinomycetes from the ancient city of Ihnasia, Egypt

  2019cites this paper
• Exo-Metabolites of Phaseolus vulgaris-Nodulating Rhizobial Strains

  2019cites this paper
• Genomic and evolutionary exploration of Asgard archaea

  2019cites this paper
• Altered metabolomic profile of dual-species biofilm: Interactions between Proteus mirabilis and Candida albicans.

  2019cites this paper
• Choosing an Optimal Sample Preparation in Caulobacter crescentus for Untargeted Metabolomics Approaches

  2019cites this paper
• Global research trends in microbiome-gut-brain axis during 2009–2018: a bibliometric and visualized study

  2019cites this paper
• Emerging molecular techniques for studying microbial community composition and function in microbiologically influenced corrosion

  2019cites this paper
• Intra- and Interspecies Variability of Single-Cell Innate Fluorescence Signature of Microbial Cell

  2019cites this paper
• Secondary Metabolites: Metabolomics for Secondary Metabolites

  2019cites this paper
• Making the Most of Trait-Based Approaches for Microbial Ecology.

  2019cites this paper
• A comprehensive look into the volatile exometabolome of enteroxic and non-enterotoxic Staphylococcus aureus strains.

  2019cites this paper
• Engineering microbial consortia by division of labor

  2019cites this paper
• Host-microbe interactions: Profiles in the transcriptome, the proteome, and the metabolome.

  2019cites this paper
• Metabolomics Analysis on the Interaction of Rice and Bacteria

  2019cites this paper
• The Use of Metabolomics and Inflammatory Mediator Profiling Provides a Novel Approach to Identifying Pediatric Appendicitis in the Emergency Department

  2018cites this paper
• Metabolomics and Biomarker Discovery in Traumatic Brain Injury

  2018cites this paper