Diet rapidly and reproducibly alters the human gut microbiome

Wu, G. D. et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105–108 (2011)

Muegge, B. D. et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332, 970–974 (2011)

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)

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

Walker, A. W. et al. Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J. 5, 220–230 (2011)

Devkota, S. et al. Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10−/− mice. Nature 487, 104–108 (2012)

Turnbaugh, P. J. et al. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci. Transl. Med. 1, 6ra14 (2009)

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

Faith, J. J., McNulty, N. P., Rey, F. E. & Gordon, J. I. Predicting a human gut microbiota’s response to diet in gnotobiotic mice. Science 333, 101–104 (2011)

Russell, W. R. et al. High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health. Am. J. Clin. Nutr. 93, 1062–1072 (2011)

Cordain, L. et al. Plant-animal subsistence ratios and macronutrient energy estimations in worldwide hunter-gatherer diets. Am. J. Clin. Nutr. 71, 682–692 (2000)

Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174–180 (2011)

De Filippo, C. et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl Acad. Sci. USA 107, 14691–14696 (2010)

Reddy, B. S. Diet and excretion of bile acids. Cancer Res. 41, 3766–3768 (1981)

Smith, E. A. & Macfarlane, G. T. Enumeration of amino acid fermenting bacteria in the human large intestine: effects of pH and starch on peptide metabolism and dissimilation of amino acids. FEMS Microbiol. Ecol. 25, 355–368 (1998)

Smith, E. A. & Macfarlane, G. T. Enumeration of human colonic bacteria producing phenolic and indolic compounds: effects of pH, carbohydrate availability and retention time on dissimilatory aromatic amino acid metabolism. J. Appl. Bacteriol. 81, 288–302 (1996)

Sinha, R. et al. High concentrations of the carcinogen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) occur in chicken but are dependent on the cooking method. Cancer Res. 55, 4516–4519 (1995)

Langille, M. G. I. et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnol. 31, 814–821 (2013)

Kanehisa, M. & Goto, S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27–30 (2000)

Pittard, J. & Wallace, B. J. Distribution and function of genes concerned with aromatic biosynthesis in Escherichia coli. J. Bacteriol. 91, 1494–1508 (1966)

Hawkes, K., O’Connell, J. F. & Jones, N. G. Hunting income patterns among the Hadza: big game, common goods, foraging goals and the evolution of the human diet. Philos. Trans. R. Soc. Lond. B Biol. Sci. 334, 243–250 (1991)

Bourdichon, F., Berger, B. & Casaregola, S. Safety demonstration of microbial food cultures (MFC) in fermented food products. Bull. Int. Dairy Fed. 455, 1–66 (2012)

Nychas, G. J. & Arkoudelos, J. S. Staphylococci: their role in fermented sausages. Soc. Appl. Bacteriol. Symp. Ser. 19, 167S–188S (1990)

McGavin, W. J. & Macfarlane, S. A. Rubus chlorotic mottle virus, a new sobemovirus infecting raspberry and bramble. Virus Res. 139, 10–13 (2009)

Zhang, T. et al. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol. 4, e3 (2006)

Yoshimoto, S. et al. Obesity-induced gut microbial metabolite promotes liver cancer through senescence secretome. Nature 499, 97–101 (2013)

Ridlon, J. M., Kang, D. J. & Hylemon, P. B. Bile salt biotransformations by human intestinal bacteria. J. Lipid Res. 47, 241–259 (2006)

Islam, K. B. et al. Bile acid is a host factor that regulates the composition of the cecal microbiota in rats. Gastroenterology 141, 1773–1781 (2011)

Maurice, C. F., Haiser, H. J. & Turnbaugh, P. J. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 152, 39–50 (2013)

Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7, 335–336 (2010)

Lewis, S. J. & Heaton, K. W. Stool form scale as a useful guide to intestinal transit time. Scand. J. Gastroenterol. 32, 920–924 (1997)

National Institutes of Health Diet History Questionnaire Version 2.0 (National Institutes of Health, Applied Research Program, National Cancer Institute, 2010)

Caporaso, J. G. et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl Acad. Sci. USA 108 (suppl. 1). 4516–4522 (2011)

Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621–1624 (2012)

DeSantis, T. Z. et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069–5072 (2006)

Jones, E. et al. SciPy: open source scientific tools for Python. (2001)

McKinney, W. Data structures for statistical computing in Python. Proc. 9th Python Sci. Conf. 51–56. (2010)

Strimmer, K. fdrtool: a versatile R package for estimating local and tail areabased false discovery rates. Bioinformatics 24, 1461–1462 (2008)

Friedman, J. & Alm, E. J. Inferring correlation networks from genomic survey data. PLoS Comput. Biol. 8, e1002687 (2012)

Turnbaugh, P. J. et al. Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc. Natl Acad. Sci. USA 107, 7503–7508 (2010)

Rey, F. E. et al. Dissecting the in vivo metabolic potential of two human gut acetogens. J. Biol. Chem. 285, 22082–22090 (2010)

Nelson, K. E. et al. A catalog of reference genomes from the human microbiome. Science 328, 994–999 (2010)

Ning, Z., Cox, A. J. & Mullikin, J. C. SSAHA: a fast search method for large DNA databases. Genome Res. 11, 1725–1729 (2001)

Abubucker, S. et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLOS Comput. Biol. 8, e1002358 (2012)

Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. 12, R60 (2011)

Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nature Methods 9, 357–359 (2012)

Markowitz, V. M. et al. IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res. 40, D115–D122 (2012)

Martin, J. et al. Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities. PLoS ONE 7, e36427 (2012)

Deplancke, B. et al. Molecular ecological analysis of the succession and diversity of sulfate-reducing bacteria in the mouse gastrointestinal tract. Appl. Environ. Microbiol. 66, 2166–2174 (2000)

Stewart, J. A., Chadwick, V. S. & Murray, A. Carriage, quantification, and predominance of methanogens and sulfate-reducing bacteria in faecal samples. Lett. Appl. Microbiol. 43, 58–63 (2006)

Porter, J. L. et al. Accurate enzymatic measurement of fecal bile acids in patients with malabsorption. J. Lab. Clin. Med. 141, 411–418 (2003)

Setchell, K. D., Lawson, A. M., Tanida, N. & Sjovall, J. General methods for the analysis of metabolic profiles of bile acids and related compounds in feces. J. Lipid Res. 24, 1085–1100 (1983)

Schoch, C. L. et al. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc. Natl Acad. Sci. USA 109, 6241–6246 (2012)

Gardes, M. & Bruns, T. D. ITS primers with enhanced specificity for basidiomycetes application to the identification of mycorrhizae and rusts. Mol. Ecol. 2, 113–118 (1993)

White, T. J., Bruns, T., Lee, S. & Taylor, J. in PCR Protocols: A Guide to Methods and Applications (eds Gelfand, D. H., Innis, M. A., Shinsky, J. J. & White, T. J. ) 315–322. (1990)

Walker, H. K., Hall, W. D., Hurst, J. W., Comstock, J. P. & Garber, A. J. Ketonuria 3rd edn (Butterworths, 1990)