Clustering was visualized for weighted and unweighted UniFrac data using principal coordinates analysis. We use the distance based Permutational Multivariate Analysis of Variance (NPMANOVA) to perform overall test of the difference between the two gold standards (samples taken 1 cm apart from the same piece of stool) and between gold standards and other sampling methods using both the weighted and unweighted UniFrac distance matrix. If the overall test gave significant results, then we used signed rank test on the proportion data to pinpoint

the taxonomic groups that showed significant differences in abundance between the two sampling methods. Acknowledgements We are grateful click here to members of the Wu and Bushman laboratories for help and suggestions. This work was supported by Human Microbiome Roadmap Demonstration Project UH2DK083981 CB-839 clinical trial (Wu, Bushman, Lewis, Co-PIs). We also acknowledge the Penn Genome Frontiers Institute and a grant with the Pennsylvania Department of Health; the Department of Health specifically disclaims responsibility

for any analyses, interpretations, or conclusions; NIH AI39368 (GDW); the Molecular Biology Core of The Center for Molecular Studies in Digestive and Liver Diseases (P30 DK050306); and The Joint Penn-CHOP Center for Digestive, Liver, and Pancreatic Medicine. We also acknowledge NIH instrument grant S10RR024525 and NIH CTSA grant UL1RR024134 from the National Center for Research Resources, and the Crohn’s and Colitis AZD3965 Foundation of America and the Howard Hughes Medical Institute. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Center for Research Resources or the National Institutes of Health. Electronic supplementary material Additional file 1: Table S1. Samples analyzed in the study of methods

for Guanylate cyclase 2C storage and DNA isolation. This table summarizes the samples studied comparing methods for storage and DNA isolation. (XLS 44 KB) Additional file 2: Table S2. Samples analyzed in the study of variable region primers. This table summarizes the samples used specifically in the analysis of different variable region primers. (XLS 30 KB) Additional file 3: Table S3. Sequences of primers used for amplification. This table contains the sequences of primers used for PCR amplification. (XLS 30 KB) Additional file 4: Table S4. Samples analyzed in the study of the cloned DNA mock community. This table summarizes the samples used in the study of the cloned DNA mock community. (XLS 34 KB) References 1. Savage DC: Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol 1977, 31:107–133.PubMedCrossRef 2. Zaneveld J, Turnbaugh PJ, Lozupone C, Ley RE, Hamady M, Gordon JI, Knight R: Host-bacterial coevolution and the search for new drug targets. Current opinion in chemical biology 2008,12(1):109–114.PubMedCrossRef 3.