Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota (original) (raw)

• Clemente, J.C., Ursell, L.K., Parfrey, L.W. & Knight, R. The impact of the gut microbiota on human health: an integrative view. Cell 148, 1258–1270 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Shafquat, A., Joice, R., Simmons, S.L. & Huttenhower, C. Functional and phylogenetic assembly of microbial communities in the human microbiome. Trends Microbiol. 22, 261–266 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Duncan, S.H. et al. Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces. Appl. Environ. Microbiol. 73, 1073–1078 (2007).
  Article CAS PubMed Google Scholar
• Duncan, S.H. et al. Effects of alternative dietary substrates on competition between human colonic bacteria in an anaerobic fermentor system. Appl. Environ. Microbiol. 69, 1136–1142 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Faust, K. & Raes, J. Microbial interactions: from networks to models. Nat. Rev. Microbiol. 10, 538–550 (2012).
  Article CAS PubMed Google Scholar
• Kanehisa, M. et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34, D354–D357 (2006).
  Article CAS PubMed Google Scholar
• Greenblum, S., Turnbaugh, P.J. & Borenstein, E. Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. Proc. Natl. Acad. Sci. USA 109, 594–599 (2012).
  Article PubMed Google Scholar
• Schellenberger, J. et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat. Protoc. 6, 1290–1307 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Thiele, I. & Palsson, B.O. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat. Protoc. 5, 93–121 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• McCloskey, D., Palsson, B.O. & Feist, A.M. Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. Mol. Syst. Biol. 9, 661 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Heinken, A. & Thiele, I. Systems biology of host-microbe metabolomics. Wiley Interdiscip. Rev. Syst. Biol. Med. 7, 195–219 (2015).
  Article PubMed PubMed Central Google Scholar
• Hamilton, J.J. & Reed, J.L. Software platforms to facilitate reconstructing genome-scale metabolic networks. Environ. Microbiol. 16, 49–59 (2014).
  Article PubMed Google Scholar
• Overbeek, R. et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33, 5691–5702 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Henry, C.S. et al. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat. Biotechnol. 28, 977–982 (2010).
  Article CAS PubMed Google Scholar
• Thorleifsson, S.G. & Thiele, I. rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks. Bioinformatics 27, 2009–2010 (2011).
  Article CAS PubMed Google Scholar
• Espey, M.G. Role of oxygen gradients in shaping redox relationships between the human intestine and its microbiota. Free Radic. Biol. Med. 55, 130–140 (2013).
  Article CAS PubMed Google Scholar
• Fleming, R.M.T., Vlassis, N., Thiele, I. & Saunders, M.A. Conditions for duality between fluxes and concentrations in biochemical networks. J. Theor. Biol. 409, 1–10 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Feist, A.M. & Palsson, B.O. The biomass objective function. Curr. Opin. Microbiol. 13, 344–349 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Gibbons, R.J. & Kapsimalis, B. Estimates of the overall rate of growth of the intestinal microflora of hamsters, guinea pigs, and mice. J. Bacteriol. 93, 510–512 (1967).
  CAS PubMed PubMed Central Google Scholar
• Barghash, A. & Helms, V. Transferring functional annotations of membrane transporters on the basis of sequence similarity and sequence motifs. BMC Bioinformatics 14, 343 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Gelfand, M.S. & Rodionov, D.A. Comparative genomics and functional annotation of bacterial transporters. Phys. Life Rev. 5, 22–49 (2008).
  Article Google Scholar
• Thiele, I. et al. A community-driven global reconstruction of human metabolism. Nat. Biotechnol. 31, 419–425 (2013).
  Article CAS PubMed Google Scholar
• Chiu, H.C., Levy, R. & Borenstein, E. Emergent biosynthetic capacity in simple microbial communities. PLoS Comput. Biol. 10, e1003695 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Mazumdar, V., Amar, S. & Segrè, D. Metabolic proximity in the order of colonization of a microbial community. PLoS One 8, e77617 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Gudmundsson, S. & Thiele, I. Computationally efficient flux variability analysis. BMC Bioinformatics 11, 489 (2010).
  Article PubMed PubMed Central Google Scholar
• Vital, M., Howe, A.C. & Tiedje, J.M. Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data. MBio 5, e00889 (2014).
  Article PubMed PubMed Central Google Scholar
• Louis, P. & Flint, H.J. Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine. FEMS Microbiol. Lett. 294, 1–8 (2009).
  Article CAS PubMed Google Scholar
• Flint, H.J., Scott, K.P., Duncan, S.H., Louis, P. & Forano, E. Microbial degradation of complex carbohydrates in the gut. Gut Microbes 3, 289–306 (2012).
  Article PubMed PubMed Central Google Scholar
• McNulty, N.P. et al. Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome. PLoS Biol. 11, e1001637 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Segers, M.E. & Lebeer, S. Towards a better understanding of Lactobacillus rhamnosus GG--host interactions. Microb. Cell Fact. 13 (Suppl. 1), S7 (2014).
  Article PubMed PubMed Central Google Scholar
• Savijoki, K., Suokko, A., Palva, A. & Varmanen, P. New convenient defined media for [(35)S]methionine labelling and proteomic analyses of probiotic lactobacilli. Lett. Appl. Microbiol. 42, 202–209 (2006).
  Article CAS PubMed Google Scholar
• Heinken, A. & Thiele, I. Anoxic conditions promote species-specific mutualism between gut microbes in silico. Appl. Environ. Microbiol. 81, 4049–4061 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Orth, J.D., Thiele, I. & Palsson, B.O. What is flux balance analysis? Nat. Biotechnol. 28, 245–248 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Doré, J. & Blottière, H. The influence of diet on the gut microbiota and its consequences for health. Curr. Opin. Biotechnol. 32, 195–199 (2015).
  Article CAS PubMed Google Scholar
• Human Microbiome Project Consortium. A framework for human microbiome research. Nature 486, 215–221 (2012).
• Claesson, M.J. et al. Gut microbiota composition correlates with diet and health in the elderly. Nature 488, 178–184 (2012).
  Article CAS PubMed Google Scholar
• Greenblum, S., Chiu, H.C., Levy, R., Carr, R. & Borenstein, E. Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities. Curr. Opin. Biotechnol. 24, 810–820 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Heinken, A. et al. Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe. J. Bacteriol. 196, 3289–3302 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Grosskopf, T. & Soyer, O.S. Synthetic microbial communities. Curr. Opin. Microbiol. 18, 72–77 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Faust, K. et al. Microbial co-occurrence relationships in the human microbiome. PLOS Comput. Biol. 8, e1002606 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Rigottier-Gois, L. Dysbiosis in inflammatory bowel diseases: the oxygen hypothesis. ISME J. 7, 1256–1261 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Manichanh, C., Borruel, N., Casellas, F. & Guarner, F. The gut microbiota in IBD. Nat. Rev. Gastroenterol. Hepatol. 9, 599–608 (2012).
  Article CAS PubMed Google Scholar
• Coyte, K.Z., Schluter, J. & Foster, K.R. The ecology of the microbiome: Networks, competition, and stability. Science 350, 663–666 (2015).
  Article CAS PubMed Google Scholar
• Schmidt, B.J. et al. GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. Bioinformatics 29, 2900–2908 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Taxis, T.M. et al. The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity. Nucleic Acids Res. 43, 9600–9612 (2015).
  CAS PubMed PubMed Central Google Scholar
• Sridharan, G.V. et al. Prediction and quantification of bioactive microbiota metabolites in the mouse gut. Nat. Commun. 5, 5492 (2014).
  Article CAS PubMed Google Scholar
• Luo, H., Lin, Y., Gao, F., Zhang, C.T. & Zhang, R. DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements. Nucleic Acids Res. 42, D574–D580 (2014).
  Article CAS PubMed Google Scholar
• Asnicar, F., Weingart, G., Tickle, T.L., Huttenhower, C. & Segata, N. Compact graphical representation of phylogenetic data and metadata with GraPhlAn. PeerJ 3, e1029 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Bauer, E., Laczny, C.C., Magnusdottir, S., Wilmes, P. & Thiele, I. Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires. Microbiome 3, 55 (2015).
  Article PubMed PubMed Central Google Scholar
• Rajilić-Stojanović, M. & de Vos, W.M. The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiol. Rev. 38, 996–1047 (2014).
  Article CAS PubMed Google Scholar
• Aziz, R.K. et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9, 75 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Cabib, E. & Leloir, L.F. The biosynthesis of trehalose phosphate. J. Biol. Chem. 231, 259–275 (1958).
  CAS PubMed Google Scholar
• Noor, E., Haraldsdóttir, H.S., Milo, R. & Fleming, R.M. Consistent estimation of Gibbs energy using component contributions. PLoS Comput. Biol. 9, e1003098 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Mattevi, A. et al. Structure of L-aspartate oxidase: implications for the succinate dehydrogenase/fumarate reductase oxidoreductase family. Structure 7, 745–756 (1999).
  Article CAS PubMed Google Scholar
• Dworkin, M. & Falkow, S. The Prokaryotes: a Handbook on the Biology of Bacteria (Springer, New York, 2006).
• Krieg, N.R. Bergey's Manual of Systematic Bacteriology vol. 4, edn. 2 (Springer, New York, 2010).
• Ravcheev, D.A. & Thiele, I. Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota. Front. Microbiol. 5, 674 (2014).
  PubMed PubMed Central Google Scholar
• Magnúsdóttir, S., Ravcheev, D., de Crécy-Lagard, V. & Thiele, I. Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes. Front. Genet. 6, 148 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Aziz, R.K. et al. SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models. PLoS One 7, e48053 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Ravcheev, D.A. & Thiele, I. Genomic analysis of the human gut microbiome suggests novel enzymes involved in quinone biosynthesis. Front. Microbiol. 7, 128 (2016).
  Article PubMed PubMed Central Google Scholar
• Shearer, M.J. & Newman, P. Recent trends in the metabolism and cell biology of vitamin K with special reference to vitamin K cycling and MK-4 biosynthesis. J. Lipid Res. 55, 345–362 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Vlassis, N., Pacheco, M.P. & Sauter, T. Fast reconstruction of compact context-specific metabolic network models. PLOS Comput. Biol. 10, e1003424 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Baldwin, E.A. et al. Effect of extraction method on quality of orange juice: hand-squeezed, commercial-fresh squeezed and processed. J. Sci. Food Agric. 92, 2029–2042 (2012).
  Article CAS PubMed Google Scholar
• Heinken, A., Sahoo, S., Fleming, R.M. & Thiele, I. Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut. Gut Microbes 4, 28–40 (2013).
  Article PubMed PubMed Central Google Scholar
• Thiele, I. et al. A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Syst. Biol. 5, 8 (2011).
  Article PubMed PubMed Central Google Scholar
• Thiele, I., Vo, T.D., Price, N.D. & Palsson, B.O. Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants. J. Bacteriol. 187, 5818–5830 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Baumler, D.J., Peplinski, R.G., Reed, J.L., Glasner, J.D. & Perna, N.T. The evolution of metabolic networks of E. coli. BMC Syst. Biol. 5, 182 (2011).
  Article PubMed PubMed Central Google Scholar
• NCBI Resource Coordinators. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 44, D7–D19 (2016).
• Meyer, F. et al. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9, 386 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Moreau, N.M. et al. Simultaneous measurement of plasma concentrations and 13C-enrichment of short-chain fatty acids, lactic acid and ketone bodies by gas chromatography coupled to mass spectrometry. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 784, 395–403 (2003).
  Article CAS PubMed Google Scholar
• Hiller, K. et al. MetaboliteDetector: comprehensive analysis tool for targeted and nontargeted GC/MS based metabolome analysis. Anal. Chem. 81, 3429–3439 (2009).
  Article CAS PubMed Google Scholar