A metagenome-wide association study of gut microbiota in type 2 diabetes

Wellen, K. E. & Hotamisligil, G. S. Inflammation, stress, and diabetes. J. Clin. Invest. 115, 1111–1119 (2005)

Risérus, U., Willett, W. C. & Hu, F. B. Dietary fats and prevention of type 2 diabetes. Prog. Lipid Res. 48, 44–51 (2009)

The Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447, 661–678 (2007)

Scott, L. J. et al. A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science 316, 1341–1345 (2007)

Musso, G., Gambino, R. & Cassader, M. Interactions between gut microbiota and host metabolism predisposing to obesity and diabetes. Annu. Rev. Med. 62, 361–380 (2011)

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

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

Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65 (2010)

The Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012)

The Human Microbiome Project Consortium. A framework for human microbiome research. Nature 486, 215–221 (2012)

Vijay-Kumar, M. et al. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 328, 228–231 (2010)

Bäckhed, F. et al. The gut microbiota as an environmental factor that regulates fat storage. Proc. Natl Acad. Sci. USA 101, 15718–15723 (2004)

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)

Bäckhed, F., Manchester, J. K., Semenkovich, C. F. & Gordon, J. I. Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc. Natl Acad. Sci. USA 104, 979–984 (2007)

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

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

Joossens, M. et al. Dysbiosis of the faecal microbiota in patients with Crohn’s disease and their unaffected relatives. Gut 60, 631–637 (2011)

Larsen, N. et al. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS ONE 5, e9085 (2010)

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

Price, A. L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nature Genet. 38, 904–909 (2006)

Woo, P. C. Y. et al. Bacteremia due to Clostridium hathewayi in a patient with acute appendicitis. J. Clin. Microbiol. 42, 5947–5949 (2004)

Elsayed, S. & Zhang, K. Bacteremia caused by Clostridium symbiosum. J. Clin. Microbiol. 42, 4390–4392 (2004)

McClean, K. L., Sheehan, G. J. & Harding, G. K. Intraabdominal infection: a review. Clin. Inf. Dis. 19, 100–116 (1994)

Brook, I. Clostridial infection in children. J. Med. Microbiol. 42, 78–82 (1995)

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)

McArdle, B. H. & Anderson, M. J. Fitting multivariate models to community data: a comment on distance-based redundancy analysis. Ecology 82, 290–297 (2001)

Yang, B. et al. Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers. BMC Bioinformatics 11 (suppl. 2). S5 (2010)

Krause, L. et al. Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res. 36, 2230–2239 (2008)

Wang, T. et al. Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. ISME J. 6, 320–329 (2012)

Biagi, E. et al. Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians. PLoS ONE 5, e10667 (2010)

Kashyap, P. & Farrugia, G. Oxidative stress: key player in gastrointestinal complications of diabetes. Neurogastroenterol. Motil. 23, 111–114 (2011)

Lyssenko, V. et al. Clinical risk factors, DNA variants, and the development of type 2 diabetes. N. Engl. J. Med. 359, 2220–2232 (2008)

Godon, J. J., Zumstein, E., Dabert, P., Habouzit, F. & Moletta, R. Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl. Environ. Microbiol. 63, 2802–2813 (1997)

Li, S. et. al. Type 2 diabetes gut metagenome (microbiome) data from 368 Chinese samples. GigaScience http://dx.doi.org/10.5524/100036 (2012)

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