Abstract
We could say that the concept of metabolomics started with microorganisms because the first published metabolome studies were focused on microbial systems and since the early 1990s, metabolite profiling has been applied to microbiology for phenotypic characterization of microbial strains and as a tool for microbial identification. This chapter presents a brief history of microbial metabolomics in the past 14 years, highlighting major breakthroughs and achievements as well as remaining technical challenges in the field. The future of microbial metabolomics will certainly depend on increasing sensitivity of analytical techniques to allow the detection and identification of intracellular metabolites using very small biomass samples. Mass spectrometry seems to be the technology with best potential to achieve this objective. Important recent steps have been taken towards this goal, meaning that single-cell microbial metabolomics could be very close to reality.
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References
Aguilar-Barajas E, Diaz-Perez C, Ramirez-Diaz MI, Riveros-Rosas H, Cervantes C (2011) Bacterial transport of sulfate, molybdate, and related oxyanions. Biometals 24:687–707
Allen J, Davey HM, Broadhurst D, Heald JK, Rowland JJ, Oliver SG, Kell DB (2003) High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nat Biotech 21:692–696
Alvarez-Martinez CE, Christie PJ (2009) Biological diversity of prokaryotic type IV secretion systems. Microbiol Mol Biol Rev 73:775–808
Andersen B, Solfrizzo M, Visconti A (1995) Metabolite profiles of common Staphylium species. Mychological Res 99:672–676
Badri DV, Zolla G, Bakker MG, Manter DK, Vivanco JM (2013) Potential impact of soil microbiomes on the leaf metabolome and on herbivore feeding behaviour. N Phytol 198:264–273
Bolten CJ et al (2007) Sampling for metabolome analysis of microorganisms. Anal Chem 79:3843–3849
Boots AW, van Berkel JJBN, Dallinga JW, Smolinska A, Wouters EF, van Schooten FJ (2012) The versatile use of exhaled volatile organic compounds in human health and disease. J Breath Res 6:027108
Bundy JG, Willey TL, Castell RS, Ellar DJ, Brindle KM (2005) Discrimination of pathogenic clinical isolates and laboratory strains of Bacillus cereus by NMR-based metabolomic profiling. FEMS Microbiol Lett 242:127–136
Canelas AB et al (2008) Leakage-free rapid quenching technique for yeast metabolomics. Metabolomics 4:226–239
Castrillo JI, Hayes A, Mohammed S, Gaskell SJ, Oliver SG (2003) An optimized protocol for metabolome analysis in yeast using direct infusion electrospray mass spectrometry. Phytochemistry 62:929–937
Cevallos-Cevallos JM, Danyluk MD, Reyes-De-Corcuera JI (2011) GC-MS based metabolomics for rapid simultaneous detection of Escherichia coli O157:H7, Salmonella Typhimurium, Salmonella Muenchen, and Salmonella Hartford in ground beef and chicken. J Food Sci 76:M238–M246
Chapon-Hervé V, Akrim M, Latifi A, Williams A, Bally M (1997) Regulation of the xcp secretion pathway by multiple quorum-sensing modulons in Pseudomonas aeruginosa Mol Microbiol 24:1169–1178
Collar C (1991) Biochemical and technological assessment of the metabolism of pure and mixed cultures of yeast and lactic acid bacteria in breadmaking applications. Food Sci Technol Int 2:349–367
Faijes M, Mars AE, Smid EJ (2007) Comparison of quenching and extraction methodologies for metabolome analysis of Lactobacillus plantarum. Microb Cell Fact 6(1):1
Fiehn O (2001) Combining genomics, metabolome analysis, and biochemical modeling to understand metabolic networks. Com Funct Genomics 2:155–168
Fiehn O (2002) Metabolomics—the link between genotypes and phenotypes. Plant Mol Biol 48:155–171
Fiehn O, Kopka J, Dormann P, Altmann T, Trethewey RN, Willmitzer L (2000) Metabolite profiling for plant functional genomics. Nat Biotechnol 18:1157–1161
Genin S, Boucher CA (1994) A superfamily of proteins involved in different secretion pathways in gram-negative bacteria: modular structure and specificity of the N-terminal domain. Mol Genomics Genet 243:112–118
Granucci N, Pinu FR, Han T-L, Villas-Bôas SG (2015) Can we predict the intracellular metabolic state of a cell based on extracellular metabolite data? Mol Biosyst 11:3297–3304
Guo AC, Jewison T, Wilson M, Liu YF, Knox C, Djoumbou Y, Lo P, Mandal R, Krishnamurthy R, Wishart DS (2013) ECMDB: the E-coli metabolome database. Nucleic Acid Res 41:D625–D630
Han J, Antunes LCM, Finlay BB, Borcherst CH (2010) Metabolomics: towards understanding host-microbe interactions. Future Microbiol 5:153–161
Hoerr V, Zbytnuik L, Leger C, Tam PPC, Kubes P, Vogel HJ (2012) Gram-negative and Gram-positive bacterial infections give rise to a different metabolic response in a mouse model. J Proteome Res 11:3231–3245
Hofman-Bang J (1999) Nitrogen catabolite repression in Saccharomyces cerevisiae. Mol Biotechnol 12:35–73
Jahangir M, Kim HK, Choi YH, Verpoorte R (2008) Metabolomic response of Brassica rapa submitted to pre-harvest bacterial contamination. Food Chem 107:362–368
Jewison T, Knox C, Neveu V, Djoumbou Y, Guo AC, Lee J, Liu P, Mandal R, Krishnamurthy R, Sinelnikov I, Wilson M, Wishart DS (2012) YMDB: the yeast metabolome database. Nucleic Acid Res 40:D815–D820
Jojima T, Omumasaba CA, Inui M, Yukawa H (2010) Sugar transporters in efficient utilization of mixed sugar substrates: current knowledge and outlook. Appl Microbiol Biotechnol 85:471–480
Kimes NE, Callaghan AV, Aktas DF, Smith WL, Sunner J, Golding BT, Drozdowska M, Hazen TC, Suflita JM, Morris PJ (2013) Metagenomic analysis and metabolite profiling of deep-sea sediments from the Gulf of Mexico following the Deepwater Horizon oil spill. Front Microbiol 4:50
Krämer R (1994) Secretion of amino acids by bacteria: physiology and mechanism. FEMS Microbiol Rev 13:75–94
Lee SY, Lee D, Kim TY (2005) Systems biotechnology for strain improvement. Trends Biotechnol 23:349–358
Lv HT (2013) Mass spectrometry-based metabolomics towards understanding of gene functions with a diversity of biological contexts. Mass Spectrom Rev 32:118–128
Maharjan RP, Ferenci T (2003) Global metabolite analysis: the influence of extraction methodology on metabolome profiles of Escherichia coli. Anal Biochem 313:145–154
Marcobal A, Kashyap PC, Nelson TA, Aronov PA, Donia MS, Spormann A, Fischbach MA, Sonnenburg JL (2013) A metabolomic view of how the human gut microbiota impacts the host metabolome using humanized and gnotobiotic mice. ISME J 7:1933–1943
Martín JF, Casqueiro J, Liras P (2005) Secretion systems for secondary metabolites: how producer cells send out messages of intracellular communication. Curr Opin Microbiol 8:282–293
Martin FPJ, Dumas ME, Wang YL, Legido-Quigley C, Yap IKS, Tang HR, Zirah S, Murphy GM, Cloarec O, Lindon JC, Sprenger N, Fay LB, Kochhar S, van Bladeren P, Holmes E, Nicholson JK (2007) A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model. Mol Syst Biol 112:112
Mashego MR, van Gulik WM, Vinke JL, Heijnen JJ (2003) Critical evaluation of sampling techniques for residual glucose determination in carbon limited chemostat culture of Saccharomyces cerevisiae. Biotech Bioeng 83:395–399
Mickiewicz B, Vogel HJ, Wong HR, Winston BW (2013) Metabolomics as a novel approach for early diagnosis of pediatric septic shock and its mortality. Am J Respir Crit Care Med 187:967–976
Ming X, Stein TTP, Barnes V, Rhodes N, Guo LN (2012) Metabolic perturbance in autism spectrum disorders: a metabolomics study. J Proteomic Res 11:5856–5862
Montel E, Bridge PD, Sutton BC (1991) An integrated approach to Phoma systematics. Mychopathologia 115:89–103
Moxley JF et al (2009) Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. Proc Natl Acad Sci USA 106:6477–6482
Nguyen QT, Merlo ME, Medema MH, Jankevics A, Breitling R, Takano E (2012) Metabolomics methods for the synthetic biology of secondary metabolism. FEBS Lett 586:2177–2183
Oliver SG (1997) Yeast as a navigational aid in genome analysis. Microbiology 7:405–409
Oliver SG, Winson MK, Kell DB, Baganz F (1998) Systematic functional analysis of the yeast genome. Trends Biotechnol 16:373–378
Ponnusamy K, Lee S, Lee CH (2013) Time-dependent correlation of the microbial community and the metabolomics of traditional Barley Nuruk starter fermentation. Biosci Biotechnol Biochem 77:683–690
Reeves ML, Rabinowtiz JD (2011) Metabolomics in systems microbiology. Curr Opin Biotechnol 22:17–25
Roessner U, Wagner C, Kopka J, Trethewey RN, Willmitzer L (2000) Simultaneous analysis of metabolites in potato tuber by gas chromatography-mass spectrometry. Plant J 23:131–142
Roessner U, Luedemann A, Brust D, Fiehn O, Linke T, Willmitzer L, Fernie AR (2001) Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. Plant Cell 13:11–29
Russell WR, Duncan SH (2013) Advanced analytical methodologies to study the microbial metabolome of the human gut. Trac-Trends Anal Chem 52:54–60
Slupsky CM (2010) NMR-based analysis of metabolites in urine provides rapid diagnosis and etiology of pneumonia. Biomark Med 4:195–197
Smedsgaard J, Frisvad JC (1996) Using direct electrospray mass spectrometry in taxonomy and secondary metabolite profiling of crude fungal extracts. J Microbiol Meth 25:5–17
Soga T, Ross GA (1999) Simultaneous determination of inorganic anions, organic acids, amino acids and carbohydrates by capillary electrophoresis. J Chromatogr A 837:231–239
Soga T, Heiger DN (2000) Amino acid analysis by capillary electrophoresis electrospray ionization mass spectrometry. Anal Chem 72:1236–1241
Soga T, Imaizumi M (2001) Capillary electrophoresis method for the analysis of inorganic anions, organic acids, amino acids, nucleotides, carbohydrates and other anionic compounds. Electrophoresis 22:3418–3425
Soga T, Ueno Y, Naraoka H, Ohashi Y, Tomita M, Nishioka T (2002a) Simultaneous determination of anionic intermediates for Bacillus subtilis metabolic pathways by capillary electrophoresis electrospray ionization mass spectrometry. Anal Chem 74:2233–2239
Soga T, Ueno Y, Naraoka H, Matsuda K, Tomita M, Nishioka T (2002b) Pressure-assisted capillary electrophoresis electrospray ionization mass spectrometry for analysis of multivalent anions. Anal Chem 74:6224–6229
Stergiopoulos I, Zwiers L-H, Waard, MAD (2002) Secretion of natural and synthetic toxic compounds from filamentous fungi by membrane transporters of the ATP-binding cassette and major facilitator superfamily. Eur J Plant Pathol 108:719–734
Storr M, Vogel HJ, Schicho R (2013) Metabolomics: is it useful for inflammatory bowel diseases? Curr Opin Gastroenterol 29:378–383
Sue T, Obolonkin V, Griffiths H, Villas-Bôas SG (2011) An exometabolomics approach to monitoring microbial contamination in microalgal fermentation processes by using metabolic footprint analysis. Appl Environ Microbiol 77:7605–7610
Tredwell GD et al (2011) The development of metabolomic sampling procedures for Pichia pastoris and baseline metabolome data. Plos One 6(1):e16286
Tweeddale H, Notley-McRobb L, Ferenci T (1998) Effect of slow growth on metabolism of Escherichia coli, as revealed by global metabolite pool (Metabolome) analysis. J Bacteriol 180:5109–5116
Tweeddale H, Notley-McRobb L, Ferenci T (1999) Assessing the effect of reactive oxygen species on Escherichia coli using a metabolome approach. Redox Rep 4:237–241
van der Werf MJ, Overkamp KM, Muilwijk B, Coulier L, Hankemeier T (2007) Microbial metabolomics: toward a platform with full metabolome coverage. Anal Biochem 370:17–25
Villas-Bôas SG, Delicado DG, Åkesson M, Nielsen J (2003) Simultaneous analysis of amino and nonamino organic acids as methyl chloroformate derivatives using gas chromatography-mass spectrometry. Anal Biochem 322:134–138
Villas-Bôas SG, Moxley JF, Åkesson M, Stephanopoulos G, Nielsen J (2005a) High-throughput metabolic state analysis: the missing link in integrated functional genomics of yeasts. Biochem J 388:669–677
Villas-Bôas SG, Højer-Pedersen J, Åkesson M, Smedsgaard J, Nielsen J (2005b) Global metabolite analysis of yeasts: evaluation of sample preparation methods. Yeast 22:1155–1169
Villas-Bôas SG, Noel S, Lane GA, Attwood G, Cookson A (2006) Extracellular metabolomics: a metabolic footprinting approach to assess fiber degradation in complex media. Anal Biochem 349:297–305
Villas-Bôas SG, Bruheim P (2007) Cold glycerol-saline: the promising quenching solution for accurate intracellular metabolite analysis of microbial cells. Anal Biochem 370:87–97
Villas-Bôas SG et al (2008) Phenotypic characterization of transposon-inserted mutants of Clostridium proteoclasticum B316T using extracellular metabolomics. J Biotech 134:55–63
Wang Q, Wu C, Chen T, Chen X, Zhao X (2006) Integrating metabolomics into systems biology framework to exploit metabolic complexity: strategies and applications in microorganisms. Appl Microbiol Biotech 70:151–161
Wittmann C, Krömer JO, Kiefer P, Binz T, Heinzle E (2004) Impact of the cold shock phenomenon on quantification of intracellular metabolites in bacteria. Anal Biochem 327:135–139
Xie BG, Waters MJ, Schirra HJ (2012) Investigating potential mechanisms of obesity by metabolomics. J Biomed Biotech #805683.
Zenobi R (2013) Single-cell metabolomics: analytical and biological perspectives. Science 342:1243259
Zhang AH, Sun H, Yan GL, Wang P, Han Y, Wang XJ (2014) Metabolomics in diagnosis and biomarker discovery of colorectal cancer. Cancer Lett 345:17–20
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Villas-Boas, S.G. (2016). Introduction to Microbial Metabolomics. In: Beale, D., Kouremenos, K., Palombo, E. (eds) Microbial Metabolomics. Springer, Cham. https://doi.org/10.1007/978-3-319-46326-1_1
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