A human gut microbial gene catalogue established by metagenomic sequencing

Ley, R. E., Peterson, D. A. & Gordon, J. I. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124, 837–848 (2006)

Backhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A. & Gordon, J. I. Host-bacterial mutualism in the human intestine. Science 307, 1915–1920 (2005)

Hooper, L. V., Midtvedt, T. & Gordon, J. I. How host-microbial interactions shape the nutrient environment of the mammalian intestine. Annu. Rev. Nutr. 22, 283–307 (2002)

Ley, R. E., Turnbaugh, P. J., Klein, S. & Gordon, J. I. Microbial ecology: human gut microbes associated with obesity. Nature 444, 1022–1023 (2006)

Turnbaugh, P. J. et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027–1031 (2006)

Ley, R. E. et al. Obesity alters gut microbial ecology. Proc. Natl Acad. Sci. USA 102, 11070–11075 (2005)

Zhang, H. et al. Human gut microbiota in obesity and after gastric bypass. Proc. Natl Acad. Sci. USA 106, 2365–2370 (2009)

Turnbaugh, P. J. et al. A core gut microbiome in obese and lean twins. Nature 457, 480–484 (2009)

Zoetendal, E. G., Akkermans, A. D. & De Vos, W. M. Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl. Environ. Microbiol. 64, 3854–3859 (1998)

Eckburg, P. B. et al. Diversity of the human intestinal microbial flora. Science 308, 1635–1638 (2005)

Ley, R. E., Lozupone, C. A., Hamady, M., Knight, R. & Gordon, J. I. Worlds within worlds: evolution of the vertebrate gut microbiota. Nature Rev. Microbiol. 6, 776–788 (2008)

Palmer, C., Bik, E. M., Digiulio, D. B., Relman, D. A. & Brown, P. O. Development of the human infant intestinal microbiota. PLoS Biol. 5, e177 (2007)

Riesenfeld, C. S., Schloss, P. D. & Handelsman, J. Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet. 38, 525–552 (2004)

von Mering, C. et al. Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315, 1126–1130 (2007)

Tringe, S. G. & Rubin, E. M. Metagenomics: DNA sequencing of environmental samples. Nature Rev. Genet. 6, 805–814 (2005)

Gill, S. R. et al. Metagenomic analysis of the human distal gut microbiome. Science 312, 1355–1359 (2006)

Kurokawa, K. et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 14, 169–181 (2007)

Suau, A. et al. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl. Environ. Microbiol. 65, 4799–4807 (1999)

Li, R. & Zhu, H. De novo assembly of the human genomes with massively parallel short read sequencing. Genome Res. 10.1101/gr.097261.109 (17 December 2009)

Noguchi, H., Park, J. & Takagi, T. MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res. 34, 5623–5630 (2006)

Colwell, R. K. EstimateS: Statistical estimation of species richness and shared species from samples, version 8.2. 〈 http://viceroy.eeb.uconn.edu/estimates 〉 (1997)

Manichanh, C. et al. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut 55, 205–211 (2006)

Wang, X., Heazlewood, S. P., Krause, D. O. & Florin, T. H. Molecular characterization of the microbial species that colonize human ileal and colonic mucosa by using 16S rDNA sequence analysis. J. Appl. Microbiol. 95, 508–520 (2003)

Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y. & Hattori, M. The KEGG resource for deciphering the genome. Nucleic Acids Res. 32, D277–D280 (2004)

Tatusov, R. L. et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41 (2003)

Jensen, L. J. et al. eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res. 36, D250–D254 (2008)

Kobayashi, K. et al. Essential Bacillus subtilis genes. Proc. Natl Acad. Sci. USA 100, 4678–4683 (2003)

Baba, T. et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 10.1038/msb4100050 (2006)

Dongowski, G., Lorenz, A. & Anger, H. Degradation of pectins with different degrees of esterification by Bacteroides thetaiotaomicron isolated from human gut flora. Appl. Environ. Microbiol. 66, 1321–1327 (2000)

Cummings, J. H. & Macfarlane, G. T. The control and consequences of bacterial fermentation in the human colon. J. Appl. Bacteriol. 70, 443–459 (1991)

Wong, J. M., de Souza, R., Kendall, C. W., Emam, A. & Jenkins, D. J. Colonic health: fermentation and short chain fatty acids. J. Clin. Gastroenterol. 40, 235–243 (2006)

Hamer, H. M. et al. The role of butyrate on colonic function. Aliment. Pharmacol. Ther. 27, 104–119 (2008)

Elango, R., Ball, R. O. & Pencharz, P. B. Amino acid requirements in humans: with a special emphasis on the metabolic availability of amino acids. Amino Acids 37, 19–27 (2009)

Metges, C. C. Contribution of microbial amino acids to amino acid homeostasis of the host. J. Nutr. 130, 1857S–1864S (2000)

Tap, J. et al. Towards the human intestinal microbiota phylogenetic core. Environ. Microbiol. 11, 2574–2584 (2009)

Kent, W. J. BLAT–the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002)

Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997)

Letunic, I., Yamada, T., Kanehisa, M. & Bork, P. iPath: interactive exploration of biochemical pathways and networks. Trends Biochem Sci. 33, 101–103 (2008)

von Mering, C. et al. STRING 7—recent developments in the integration and prediction of protein interactions. Nucleic Acids Res. 35, D358–D362 (2007)

Toft, U. et al. The impact of a population-based multi-factorial lifestyle intervention on changes in long-term dietary habits: The Inter99 study. Prev. Med. 47, 378–383 (2008)

Li, R. et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25, 1966–1967 (2009)

Huson, D. H., Auch, A. F., Qi, J. & Schuster, S. C. MEGAN analysis of metagenomic data. Genome Res. 17, 377–386 (2007)

van Dongen, S. Graph Clustering by Flow Simulation. PhD thesis, Univ. Utrecht (2000)

Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003)