references.bib

@article{RN110,
   author = {Caporaso, J. G. and Kuczynski, J. and Stombaugh, J. and Bittinger, K. and Bushman, F. D. and Costello, E. K. and Fierer, N. and Pena, A. G. and Goodrich, J. K. and Gordon, J. I. and Huttley, G. A. and Kelley, S. T. and Knights, D. and Koenig, J. E. and Ley, R. E. and Lozupone, C. A. and McDonald, D. and Muegge, B. D. and Pirrung, M. and Reeder, J. and Sevinsky, J. R. and Turnbaugh, P. J. and Walters, W. A. and Widmann, J. and Yatsunenko, T. and Zaneveld, J. and Knight, R.},
   title = {QIIME allows analysis of high-throughput community sequencing data},
   journal = {Nature Methods},
   volume = {7},
   number = {5},
   pages = {335-6},
   ISSN = {1548-7105 (Electronic) 1548-7091 (Linking)},
   DOI = {10.1038/nmeth.f.303},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20383131},
   year = {2010},
   type = {Journal Article}
}

@article{RN85,
   author = {Caporaso, J. G. and Lauber, C. L. and Costello, E. K. and Berg-Lyons, D. and Gonzalez, A. and Stombaugh, J. and Knights, D. and Gajer, P. and Ravel, J. and Fierer, N. and Gordon, J. I. and Knight, R.},
   title = {Moving pictures of the human microbiome},
   journal = {Genome Biol},
   volume = {12},
   number = {5},
   pages = {R50},
   ISSN = {1465-6914 (Electronic) 1465-6906 (Linking)},
   DOI = {10.1186/gb-2011-12-5-r50},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21624126},
   year = {2011},
   type = {Journal Article}
}

@article{RN111,
   author = {Chen, Vincent B. and Davis, Ian W. and Richardson, David C.},
   title = {KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program},
   journal = {Protein Science},
   volume = {18},
   number = {11},
   pages = {2403-2409},
   ISSN = {1469-896X},
   DOI = {10.1002/pro.250},
   url = {http://dx.doi.org/10.1002/pro.250},
   year = {2009},
   type = {Journal Article}
}

@article{RN82,
   author = {Finegold, S. M. and Dowd, S. E. and Gontcharova, V. and Liu, C. and Henley, K. E. and Wolcott, R. D. and Youn, E. and Summanen, P. H. and Granpeesheh, D. and Dixon, D. and Liu, M. and Molitoris, D. R. and Green, J. A., 3rd},
   title = {Pyrosequencing study of fecal microflora of autistic and control children},
   journal = {Anaerobe},
   volume = {16},
   number = {4},
   pages = {444-53},
   ISSN = {1095-8274 (Electronic)
1075-9964 (Linking)},
   DOI = {10.1016/j.anaerobe.2010.06.008},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20603222},
   year = {2010},
   type = {Journal Article}
}

@article{RN10,
   author = {Gilbert, J. A. and Meyer, F. and Antonopoulos, D. and Balaji, P. and Brown, C. T. and Desai, N. and Eisen, J. A. and Evers, D. and Field, D. and Feng, W. and Huson, D. and Jansson, J. and Knight, R. and Knight, J. and Kolker, E. and Konstantindis, K. and Kostka, J. and Kyrpides, N. and Mackelprang, R. and McHardy, A. and Quince, C. and Raes, J. and Sczyrba, A. and Shade, A. and Stevens, R.},
   title = {Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project},
   journal = {Stand Genomic Sci},
   volume = {3},
   number = {3},
   pages = {243-8},
   ISSN = {1944-3277 (Electronic)
1944-3277 (Linking)},
   DOI = {10.4056/sigs.1433550},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21304727},
   year = {2010},
   type = {Journal Article}
}

@article{RN53,
   author = {Gonzalez, A. and Knight, R.},
   title = {Advancing analytical algorithms and pipelines for billions of microbial sequences},
   journal = {Current opinion in biotechnology},
   volume = {23},
   number = {1},
   pages = {64-71},
   ISSN = {1879-0429 (Electronic)
0958-1669 (Linking)},
   DOI = {10.1016/j.copbio.2011.11.028},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22172529},
   year = {2012},
   type = {Journal Article}
}

@article{RN109,
   author = {Gower, J. C. and Legendre, P.},
   title = {Metric and Euclidean properties of dissimilarity coefficients},
   journal = {Journal of Classification},
   volume = {3},
   number = {1},
   pages = {5-48},
   ISSN = {0176-4268},
   DOI = {10.1007/bf01896809},
   url = {http://dx.doi.org/10.1007/BF01896809},
   year = {1986},
   type = {Journal Article}
}

@article{RN115,
   author = {Harris, Roger},
   title = {The L4 time-series: the first 20 years},
   journal = {Journal of Plankton Research},
   volume = {32},
   number = {5},
   pages = {577-583},
   DOI = {10.1093/plankt/fbq021},
   url = {http://plankt.oxfordjournals.org/content/32/5/577.short},
   year = {2010},
   type = {Journal Article}
}

@article{RN130,
   author = {Hewitt, K. M. and Mannino, F. L. and Gonzalez, A. and Chase, J. H. and Caporaso, J. G. and Knight, R. and Kelley, S. T.},
   title = {Bacterial diversity in two Neonatal Intensive Care Units (NICUs)},
   journal = {PLoS One},
   volume = {8},
   number = {1},
   pages = {e54703},
   ISSN = {1932-6203 (Electronic)
1932-6203 (Linking)},
   DOI = {10.1371/journal.pone.0054703},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23372757},
   year = {2013},
   type = {Journal Article}
}

@article{RN35,
   author = {HMP-Consortium},
   title = {Structure, function and diversity of the healthy human microbiome},
   journal = {Nature},
   volume = {486},
   number = {7402},
   pages = {207-14},
   ISSN = {1476-4687 (Electronic)
0028-0836 (Linking)},
   DOI = {10.1038/nature11234},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22699609},
   year = {2012},
   type = {Journal Article}
}

@article{RN112,
   author = {Hunter, J. D.},
   title = {Matplotlib: A 2D Graphics Environment},
   journal = {Computing in Science \& Engineering},
   volume = {9},
   number = {3},
   pages = {90-95},
   ISSN = {1521-9615},
   DOI = {10.1109/mcse.2007.55},
   year = {2007},
   type = {Journal Article}
}

@article{RN113,
   author = {Knight, R. and Maxwell, P. and Birmingham, A. and Carnes, J. and Caporaso, J. G. and Easton, B. C. and Eaton, M. and Hamady, M. and Lindsay, H. and Liu, Z. and Lozupone, C. and McDonald, D. and Robeson, M. and Sammut, R. and Smit, S. and Wakefield, M. J. and Widmann, J. and Wikman, S. and Wilson, S. and Ying, H. and Huttley, G. A.},
   title = {PyCogent: a toolkit for making sense from sequence},
   journal = {Genome Biol},
   volume = {8},
   number = {8},
   pages = {R171},
   ISSN = {1465-6914 (Electronic)
1465-6906 (Linking)},
   DOI = {10.1186/gb-2007-8-8-r171},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17708774},
   year = {2007},
   type = {Journal Article}
}

@article{RN11,
   author = {Koenig, J. E. and Spor, A. and Scalfone, N. and Fricker, A. D. and Stombaugh, J. and Knight, R. and Angenent, L. T. and Ley, R. E.},
   title = {Succession of microbial consortia in the developing infant gut microbiome},
   journal = {Proc Natl Acad Sci U S A},
   volume = {108 Suppl 1},
   pages = {4578-85},
   ISSN = {1091-6490 (Electronic)
0027-8424 (Linking)},
   DOI = {10.1073/pnas.1000081107},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20668239},
   year = {2011},
   type = {Journal Article}
}

@article{RN131,
   author = {Kuczynski, J. and Stombaugh, J. and Walters, W. A. and Gonzalez, A. and Caporaso, J. G. and Knight, R.},
   title = {Using QIIME to analyze 16S rRNA gene sequences from microbial communities},
   journal = {Curr Protoc Microbiol},
   volume = {Chapter 1},
   pages = {Unit 1E 5},
   ISSN = {1934-8533 (Electronic)},
   DOI = {10.1002/9780471729259.mc01e05s27},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23184592},
   year = {2012},
   type = {Journal Article}
}

@article{RN108,
   author = {Lauber, C. L. and Hamady, M. and Knight, R. and Fierer, N.},
   title = {Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale},
   journal = {Applied and Environmental Microbiology},
   volume = {75},
   number = {15},
   pages = {5111-20},
   ISSN = {1098-5336 (Electronic)
0099-2240 (Linking)},
   DOI = {10.1128/AEM.00335-09},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19502440},
   year = {2009},
   type = {Journal Article}
}

@misc{RN119,
   howpublished={\url{http://office.microsoft.com/en-us/excel/}},
   url = {http://office.microsoft.com/en-us/excel/},
   title = {Microsoft Excel},
   year = {2011},
   type = {Computer Program}
}

@article{RN114,
   author = {Muegge, B. D. and Kuczynski, J. and Knights, D. and Clemente, J. C. and Gonzalez, A. and Fontana, L. and Henrissat, B. and Knight, R. and Gordon, J. I.},
   title = {Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans},
   journal = {Science},
   volume = {332},
   number = {6032},
   pages = {970-4},
   ISSN = {1095-9203 (Electronic)
0036-8075 (Linking)},
   DOI = {10.1126/science.1198719},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21596990},
   year = {2011},
   type = {Journal Article}
}

@article{RN126,
   author = {O'Donoghue, S. I. and Gavin, A. C. and Gehlenborg, N. and Goodsell, D. S. and Heriche, J. K. and Nielsen, C. B. and North, C. and Olson, A. J. and Procter, J. B. and Shattuck, D. W. and Walter, T. and Wong, B.},
   title = {Visualizing biological data-now and in the future},
   journal = {Nature Methods},
   volume = {7},
   number = {3 Suppl},
   pages = {S2-4},
   ISSN = {1548-7105 (Electronic)
1548-7091 (Linking)},
   DOI = {10.1038/nmeth.f.301},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20195254},
   year = {2010},
   type = {Journal Article}
}

@misc{RN117,
   ISBN = {ISBN 3-900051-07-0},
   howpublished={\url{http://www.r-project.org/}},
   title = {The R Programming Language},
   year = {2013},
   type = {Computer Program}
}

@misc{RN121,
   url = {http://www.mathworks.com/products/matlab/},
   howpublished={\url{http://www.mathworks.com/products/matlab/}},
   title = {MATLAB},
   year = {2013},
   type = {Computer Program}
}

@misc{RN120,
   title = {Spotfire},
   url = {http://spotfire.tibco.com/},
   howpublished={\url{http://spotfire.tibco.com/}},
   year = {2013},
   type = {Computer Program}
}

@misc{RN132,
   title = {Emperor dataset},
   DOI= {http://dx.doi.org/10.5524/100068},
   howpublished={\url{http://dx.doi.org/10.5524/100068}},
   year = {2013},
   type = {Dataset}
}

@misc{RN118,
   title = {Wolfram Mathematica},
   url = {http://www.wolfram.com/},
   howpublished={\url{http://www.wolfram.com/}},
   year = {2010},
   type = {Computer Program}
}

@article{RN4020,
   author = {Costello, E. K. and Stagaman, K. and Dethlefsen, L. and Bohannan, B. J. and Relman, D. A.},
   title = {The application of ecological theory toward an understanding of the human microbiome},
   journal = {Science},
   volume = {336},
   number = {6086},
   pages = {1255-62},
   ISSN = {1095-9203 (Electronic)
0036-8075 (Linking)},
   DOI = {10.1126/science.1224203},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22674335},
   year = {2012},
   type = {Journal Article}
}

@article{RN4021,
   author = {David, L. A. and Materna, A. C. and Friedman, J. and Campos-Baptista, M. I. and Blackburn, M. C. and Perrotta, A. and Erdman, S. E. and Alm, E. J.},
   title = {Host lifestyle affects human microbiota on daily timescales},
   journal = {Genome Biol},
   volume = {15},
   number = {7},
   pages = {R89},
   ISSN = {1474-760X (Electronic)
1474-7596 (Linking)},
   DOI = {10.1186/gb-2014-15-7-r89},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/25146375},
   year = {2014},
   type = {Journal Article}
}

@article{RN4029,
   author = {Faust, K. and Lahti, L. and Gonze, D. and de Vos, W. M. and Raes, J.},
   title = {Metagenomics meets time series analysis: unraveling microbial community dynamics},
   journal = {Curr Opin Microbiol},
   volume = {25},
   pages = {56-66},
   ISSN = {1879-0364 (Electronic)
1369-5274 (Linking)},
   DOI = {10.1016/j.mib.2015.04.004},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/26005845},
   year = {2015},
   type = {Journal Article}
}

@article{RN4022,
   author = {Flores, G. E. and Caporaso, J. G. and Henley, J. B. and Rideout, J. R. and Domogala, D. and Chase, J. and Leff, J. W. and Vazquez-Baeza, Y. and Gonzalez, A. and Knight, R. and Dunn, R. R. and Fierer, N.},
   title = {Temporal variability is a personalized feature of the human microbiome},
   journal = {Genome Biol},
   volume = {15},
   number = {12},
   pages = {531},
   ISSN = {1474-760X (Electronic)
1474-7596 (Linking)},
   DOI = {10.1186/s13059-014-0531-y},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/25517225},
   year = {2014},
   type = {Journal Article}
}

@article{RN3802,
   author = {Kuczynski, J. and Liu, Z. and Lozupone, C. and McDonald, D. and Fierer, N. and Knight, R.},
   title = {Microbial community resemblance methods differ in their ability to detect biologically relevant patterns},
   journal = {Nat Methods},
   volume = {7},
   number = {10},
   pages = {813-9},
   ISSN = {1548-7105 (Electronic)
1548-7091 (Linking)},
   DOI = {10.1038/nmeth.1499},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20818378},
   year = {2010},
   type = {Journal Article}
}

@article{RN4025,
   author = {Lozupone, C. A. and Stombaugh, J. and Gonzalez, A. and Ackermann, G. and Wendel, D. and Vazquez-Baeza, Y. and Jansson, J. K. and Gordon, J. I. and Knight, R.},
   title = {Meta-analyses of studies of the human microbiota},
   journal = {Genome Res},
   volume = {23},
   number = {10},
   pages = {1704-14},
   ISSN = {1549-5469 (Electronic)
1088-9051 (Linking)},
   DOI = {10.1101/gr.151803.112},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23861384},
   year = {2013},
   type = {Journal Article}
}

@article{RN162,
   author = {Perez, F. and Granger, B. E.},
   title = {IPython: A system for interactive scientific computing},
   journal = {Computing in Science \& Engineering},
   volume = {9},
   number = {3},
   pages = {21-29},
   ISSN = {1521-9615},
   DOI = {Doi 10.1109/Mcse.2007.53},
   url = {<Go to ISI>://WOS:000245668100005},
   year = {2007},
   type = {Journal Article}
}

@article{RN4030,
   author = {Qin, J. and Li, R. and Raes, J. and Arumugam, M. and Burgdorf, K. S. and Manichanh, C. and Nielsen, T. and Pons, N. and Levenez, F. and Yamada, T. and Mende, D. R. and Li, J. and Xu, J. and Li, S. and Li, D. and Cao, J. and Wang, B. and Liang, H. and Zheng, H. and Xie, Y. and Tap, J. and Lepage, P. and Bertalan, M. and Batto, J. M. and Hansen, T. and Le Paslier, D. and Linneberg, A. and Nielsen, H. B. and Pelletier, E. and Renault, P. and Sicheritz-Ponten, T. and Turner, K. and Zhu, H. and Yu, C. and Li, S. and Jian, M. and Zhou, Y. and Li, Y. and Zhang, X. and Li, S. and Qin, N. and Yang, H. and Wang, J. and Brunak, S. and Dore, J. and Guarner, F. and Kristiansen, K. and Pedersen, O. and Parkhill, J. and Weissenbach, J. and Meta, H. I. T. Consortium and Bork, P. and Ehrlich, S. D. and Wang, J.},
   title = {A human gut microbial gene catalogue established by metagenomic sequencing},
   journal = {Nature},
   volume = {464},
   number = {7285},
   pages = {59-65},
   ISSN = {1476-4687 (Electronic)
0028-0836 (Linking)},
   DOI = {10.1038/nature08821},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/20203603},
   year = {2010},
   type = {Journal Article}
}

@article{RN3983,
   author = {Castellarin, M. and Warren, R. L. and Freeman, J. D. and Dreolini, L. and Krzywinski, M. and Strauss, J. and Barnes, R. and Watson, P. and Allen-Vercoe, E. and Moore, R. A. and Holt, R. A.},
   title = {Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma},
   journal = {Genome Res},
   volume = {22},
   number = {2},
   pages = {299-306},
   ISSN = {1549-5469 (Electronic)
1088-9051 (Linking)},
   DOI = {10.1101/gr.126516.111},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22009989},
   year = {2012},
   type = {Journal Article}
}

@article{RN174,
   author = {Day, M. J. and Bilzer, T. and Mansell, J. and Wilcock, B. and Hall, E. J. and Jergens, A. and Minami, T. and Willard, M. and Washabau, R. and World Small Animal Veterinary Association Gastrointestinal Standardization, Group},
   title = {Histopathological standards for the diagnosis of gastrointestinal inflammation in endoscopic biopsy samples from the dog and cat: a report from the World Small Animal Veterinary Association Gastrointestinal Standardization Group},
   journal = {J Comp Pathol},
   volume = {138 Suppl 1},
   pages = {S1-43},
   ISSN = {0021-9975 (Print)
0021-9975 (Linking)},
   DOI = {10.1016/j.jcpa.2008.01.001},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18336828},
   year = {2008},
   type = {Journal Article}
}

@article{RN3999,
   author = {Frank, D. N. and Robertson, C. E. and Hamm, C. M. and Kpadeh, Z. and Zhang, T. and Chen, H. and Zhu, W. and Sartor, R. B. and Boedeker, E. C. and Harpaz, N. and Pace, N. R. and Li, E.},
   title = {Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases},
   journal = {Inflamm Bowel Dis},
   volume = {17},
   number = {1},
   pages = {179-84},
   ISSN = {1536-4844 (Electronic)
1078-0998 (Linking)},
   DOI = {10.1002/ibd.21339},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20839241},
   year = {2011},
   type = {Journal Article}
}

@article{RN154,
   author = {Gevers, D. and Kugathasan, S. and Denson, L. A. and Vazquez-Baeza, Y. and Van Treuren, W. and Ren, B. and Schwager, E. and Knights, D. and Song, S. J. and Yassour, M. and Morgan, X. C. and Kostic, A. D. and Luo, C. and Gonzalez, A. and McDonald, D. and Haberman, Y. and Walters, T. and Baker, S. and Rosh, J. and Stephens, M. and Heyman, M. and Markowitz, J. and Baldassano, R. and Griffiths, A. and Sylvester, F. and Mack, D. and Kim, S. and Crandall, W. and Hyams, J. and Huttenhower, C. and Knight, R. and Xavier, R. J.},
   title = {The treatment-naive microbiome in new-onset Crohn's disease},
   journal = {Cell Host Microbe},
   volume = {15},
   number = {3},
   pages = {382-92},
   ISSN = {1934-6069 (Electronic)
1931-3128 (Linking)},
   DOI = {10.1016/j.chom.2014.02.005},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/24629344},
   year = {2014},
   type = {Journal Article}
}

@article{RN144,
   author = {Hayward, J. J. and Castelhano, M. G. and Oliveira, K. C. and Corey, E. and Balkman, C. and Baxter, T. L. and Casal, M. L. and Center, S. A. and Fang, M. and Garrison, S. J. and Kalla, S. E. and Korniliev, P. and Kotlikoff, M. I. and Moise, N. S. and Shannon, L. M. and Simpson, K. W. and Sutter, N. B. and Todhunter, R. J. and Boyko, A. R.},
   title = {Complex disease and phenotype mapping in the domestic dog},
   journal = {Nat Commun},
   volume = {7},
   pages = {10460},
   ISSN = {2041-1723 (Electronic)
2041-1723 (Linking)},
   DOI = {10.1038/ncomms10460},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/26795439},
   year = {2016},
   type = {Journal Article}
}

@article{RN3988,
   author = {Hedges, S. B. and Marin, J. and Suleski, M. and Paymer, M. and Kumar, S.},
   title = {Tree of life reveals clock-like speciation and diversification},
   journal = {Mol Biol Evol},
   volume = {32},
   number = {4},
   pages = {835-45},
   ISSN = {1537-1719 (Electronic)
0737-4038 (Linking)},
   DOI = {10.1093/molbev/msv037},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/25739733},
   year = {2015},
   type = {Journal Article}
}

@article{RN147,
   author = {Honneffer, J. B. and Minamoto, Y. and Suchodolski, J. S.},
   title = {Microbiota alterations in acute and chronic gastrointestinal inflammation of cats and dogs},
   journal = {World J Gastroenterol},
   volume = {20},
   number = {44},
   pages = {16489-97},
   ISSN = {2219-2840 (Electronic)
1007-9327 (Linking)},
   DOI = {10.3748/wjg.v20.i44.16489},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/25469017},
   year = {2014},
   type = {Journal Article}
}

@article{RN17472,
   author = {Langille, M. G. and Zaneveld, J. and Caporaso, J. G. and McDonald, D. and Knights, D. and Reyes, J. A. and Clemente, J. C. and Burkepile, D. E. and Vega Thurber, R. L. and Knight, R. and Beiko, R. G. and Huttenhower, C.},
   title = {Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences},
   journal = {Nat Biotechnol},
   volume = {31},
   number = {9},
   pages = {814-21},
   ISSN = {1546-1696 (Electronic)
1087-0156 (Linking)},
   DOI = {10.1038/nbt.2676},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23975157},
   year = {2013},
   type = {Journal Article}
}

@article{RN8250,
   author = {Ley, R. E. and Hamady, M. and Lozupone, C. and Turnbaugh, P. J. and Ramey, R. R. and Bircher, J. S. and Schlegel, M. L. and Tucker, T. A. and Schrenzel, M. D. and Knight, R. and Gordon, J. I.},
   title = {Evolution of mammals and their gut microbes},
   journal = {Science},
   volume = {320},
   number = {5883},
   pages = {1647-1651},
   url = {PM:18497261},
   year = {2008},
   type = {Journal Article}
}

@article{RN17583,
   author = {Mardini, H. E. and Grigorian, A. Y.},
   title = {Probiotic mix VSL\#3 is effective adjunctive therapy for mild to moderately active ulcerative colitis: a meta-analysis},
   journal = {Inflamm Bowel Dis},
   volume = {20},
   number = {9},
   pages = {1562-7},
   ISSN = {1536-4844 (Electronic)
1078-0998 (Linking)},
   DOI = {10.1097/MIB.0000000000000084},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/24918321},
   year = {2014},
   type = {Journal Article}
}

@article{RN3987,
   author = {Price, S. A. and Hopkins, S. S. and Smith, K. K. and Roth, V. L.},
   title = {Tempo of trophic evolution and its impact on mammalian diversification},
   journal = {Proc Natl Acad Sci U S A},
   volume = {109},
   number = {18},
   pages = {7008-12},
   ISSN = {1091-6490 (Electronic)
0027-8424 (Linking)},
   DOI = {10.1073/pnas.1117133109},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22509033},
   year = {2012},
   type = {Journal Article}
}

@article{RN17357,
   author = {Rossi, G. and Pengo, G. and Caldin, M. and Palumbo Piccionello, A. and Steiner, J. M. and Cohen, N. D. and Jergens, A. E. and Suchodolski, J. S.},
   title = {Comparison of Microbiological, Histological, and Immunomodulatory Parameters in Response to Treatment with Either Combination Therapy with Prednisone and Metronidazole or Probiotic VSL\#3 Strains in Dogs with Idiopathic Inflammatory Bowel Disease},
   journal = {Plos ONE},
   volume = {9},
   number = {4},
   pages = {e94699},
   ISSN = {1932-6203 (Electronic)
1932-6203 (Linking)},
   DOI = {10.1371/journal.pone.0094699},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/24722235},
   year = {2014},
   type = {Journal Article}
}

@article{RN146,
   author = {Simpson, K. W. and Dogan, B. and Rishniw, M. and Goldstein, R. E. and Klaessig, S. and McDonough, P. L. and German, A. J. and Yates, R. M. and Russell, D. G. and Johnson, S. E. and Berg, D. E. and Harel, J. and Bruant, G. and McDonough, S. P. and Schukken, Y. H.},
   title = {Adherent and invasive Escherichia coli is associated with granulomatous colitis in boxer dogs},
   journal = {Infect Immun},
   volume = {74},
   number = {8},
   pages = {4778-92},
   ISSN = {0019-9567 (Print)
0019-9567 (Linking)},
   DOI = {10.1128/IAI.00067-06},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16861666},
   year = {2006},
   type = {Journal Article}
}

@article{RN150,
   author = {Suchodolski, J. S. and Camacho, J. and Steiner, J. M.},
   title = {Analysis of bacterial diversity in the canine duodenum, jejunum, ileum, and colon by comparative 16S rRNA gene analysis},
   journal = {FEMS Microbiol Ecol},
   volume = {66},
   number = {3},
   pages = {567-78},
   ISSN = {0168-6496 (Print)
0168-6496 (Linking)},
   DOI = {10.1111/j.1574-6941.2008.00521.x},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18557939},
   year = {2008},
   type = {Journal Article}
}

@article{RN17268,
   author = {Suchodolski, J. S. and Dowd, S. E. and Wilke, V. and Steiner, J. M. and Jergens, A. E.},
   title = {16S rRNA gene pyrosequencing reveals bacterial dysbiosis in the duodenum of dogs with idiopathic inflammatory bowel disease},
   journal = {Plos ONE},
   volume = {7},
   number = {6},
   pages = {e39333},
   ISSN = {1932-6203 (Electronic)
1932-6203 (Linking)},
   DOI = {10.1371/journal.pone.0039333},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22720094},
   year = {2012},
   type = {Journal Article}
}

@article{RN17138,
   author = {Suchodolski, J. S. and Markel, M. E. and Garcia-Mazcorro, J. F. and Unterer, S. and Heilmann, R. M. and Dowd, S. E. and Kachroo, P. and Ivanov, I. and Minamoto, Y. and Dillman, E. M. and Steiner, J. M. and Cook, A. K. and Toresson, L.},
   title = {The fecal microbiome in dogs with acute diarrhea and idiopathic inflammatory bowel disease},
   journal = {Plos ONE},
   volume = {7},
   number = {12},
   pages = {e51907},
   ISSN = {1932-6203 (Electronic)
1932-6203 (Linking)},
   DOI = {10.1371/journal.pone.0051907},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23300577},
   year = {2012},
   type = {Journal Article}
}

@article{RN158,
   author = {Uronis, J. M. and Arthur, J. C. and Keku, T. and Fodor, A. and Carroll, I. M. and Cruz, M. L. and Appleyard, C. B. and Jobin, C.},
   title = {Gut microbial diversity is reduced by the probiotic VSL\#3 and correlates with decreased TNBS-induced colitis},
   journal = {Inflamm Bowel Dis},
   volume = {17},
   number = {1},
   pages = {289-97},
   ISSN = {1536-4844 (Electronic)
1078-0998 (Linking)},
   DOI = {10.1002/ibd.21366},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20564535},
   year = {2011},
   type = {Journal Article}
}

@article{RN3989,
   author = {Wesley-Hunt, G. D.; Flynn, J. J.},
   title = {Phylogeny of the Carnivora: Basal relationships among the carnivoramorphans, and assessment of the position of 'Miacoidea' relative to Carnivora},
   journal = {Journal of Systematic Palaeontology},
   volume = {3},
   number = {1},
   pages = {1-28},
   ISSN = {1477-2019},
   url = {<Go to ISI>://WOS:000229236300001},
   year = {2005},
   type = {Journal Article}
}

@misc{RN164,
   title = {The Earth Microbiome Project Standard Protocols},
   howpublished={\url{http://www.earthmicrobiome.org/emp-standard-protocols/}},
   url = {http://www.earthmicrobiome.org/emp-standard-protocols/},
   year = {2015},
   type = {Web Page}
}

@article{RN3986,
   author = {Kuhn, M.},
   title = {Building Predictive Models in R Using the caret Package},
   journal = {Journal of Statistical Software},
   volume = {28},
   number = {5},
   pages = {1-26},
   ISSN = {1548-7660},
   url = {<Go to ISI>://WOS:000260799600001},
   year = {2008},
   type = {Journal Article}
}

@article{RN4000,
   author = {Mawby, D. I. and Bartges, J. W. and d'Avignon, A. and Laflamme, D. P. and Moyers, T. D. and Cottrell, T.},
   title = {Comparison of various methods for estimating body fat in dogs},
   journal = {J Am Anim Hosp Assoc},
   volume = {40},
   number = {2},
   pages = {109-14},
   ISSN = {1547-3317 (Electronic)
0587-2871 (Linking)},
   DOI = {10.5326/0400109},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15007045},
   year = {2004},
   type = {Journal Article}
}

@article{RN165,
   author = {McDonald, D. and Price, M. N. and Goodrich, J. and Nawrocki, E. P. and DeSantis, T. Z. and Probst, A. and Andersen, G. L. and Knight, R. and Hugenholtz, P.},
   title = {An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea},
   journal = {ISME J},
   volume = {6},
   number = {3},
   pages = {610-8},
   ISSN = {1751-7370 (Electronic)
1751-7362 (Linking)},
   DOI = {10.1038/ismej.2011.139},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22134646},
   year = {2012},
   type = {Journal Article}
}

@article{RN168,
   author = {Schwager, E and Huttenhower, C},
   title = {Detecting statistically significant associtations between sparse and high dimensional compositional data.},
   journal = {Unpublished},
   year = {2016},
   type = {Journal Article}
}

@article{RN169,
   author = {Shannon, P. and Markiel, A. and Ozier, O. and Baliga, N. S. and Wang, J. T. and Ramage, D. and Amin, N. and Schwikowski, B. and Ideker, T.},
   title = {Cytoscape: a software environment for integrated models of biomolecular interaction networks},
   journal = {Genome Res},
   volume = {13},
   number = {11},
   pages = {2498-504},
   ISSN = {1088-9051 (Print)
1088-9051 (Linking)},
   DOI = {10.1101/gr.1239303},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/14597658},
   year = {2003},
   type = {Journal Article}
}

@article{RN3985,
   author = {Stone, L. and Roberts, A.},
   title = {The Checkerboard Score and Species Distributions},
   journal = {Oecologia},
   volume = {85},
   number = {1},
   pages = {74-79},
   ISSN = {0029-8549},
   DOI = {Doi 10.1007/Bf00317345},
   url = {<Go to ISI>://WOS:A1990EJ23000010},
   year = {1990},
   type = {Journal Article}
}

@article{RN3823,
   author = {van der Walt, S. and Colbert, S. C. and Varoquaux, G.},
   title = {The NumPy Array: A Structure for Efficient Numerical Computation},
   journal = {Computing in Science \& Engineering},
   volume = {13},
   number = {2},
   pages = {22-30},
   ISSN = {1521-9615},
   url = {<Go to ISI>://WOS:000288053300003},
   year = {2011},
   type = {Journal Article}
}

@article{RN170,
   author = {Waskom, M},
   title = {Seaborn: statistical data visualization},
   url = {https://stanford.edu/~mwaskom/software/seaborn/introduction.html},
   year = {2012},
   type = {Journal Article}
}

@article{RN167,
   author = {Weiss, S. J. and Xu, Z. and Amir, A. and Peddada, S.; Bittinger, K. and Gonzalez, A. and Lozupone, C. and Zaneveld, J. R. and Vazquez-Baeza, Y. and Birmingham, A. and Knight, R},
   title = {Effects of library size variance, sparsity, and compositionality on the analysis of microbiome data},
   journal = {PeerJ Pre-print},
   year = {2015},
   type = {Journal Article}
}

Uncategorized References
@article{RN17324,
   author = {Jergens, A. E. and Simpson, K. W.},
   title = {Inflammatory bowel disease in veterinary medicine},
   journal = {Front Biosci (Elite Ed)},
   volume = {4},
   pages = {1404-19},
   ISSN = {1945-0508 (Electronic)
1945-0494 (Linking)},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22201965},
   year = {2012},
   type = {Journal Article}
}

@article{RN153,
   author = {Minamoto, Y. and Otoni, C. C. and Steelman, S. M. and Buyukleblebici, O. and Steiner, J. M. and Jergens, A. E. and Suchodolski, J. S.},
   title = {Alteration of the fecal microbiota and serum metabolite profiles in dogs with idiopathic inflammatory bowel disease},
   journal = {Gut Microbes},
   volume = {6},
   number = {1},
   pages = {33-47},
   ISSN = {1949-0984 (Electronic)
1949-0976 (Linking)},
   DOI = {10.1080/19490976.2014.997612},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/25531678},
   year = {2015},
   type = {Journal Article}
}

References

@article{RN4132,
   author = {Alang, N. and Kelly, C. R.},
   title = {Weight gain after fecal microbiota transplantation},
   journal = {Open Forum Infect Dis},
   volume = {2},
   number = {1},
   pages = {ofv004},
   ISSN = {2328-8957 (Linking)},
   DOI = {10.1093/ofid/ofv004},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/26034755},
   year = {2015},
   type = {Journal Article}
}

@article{RN4071,
   author = {Amieva, M. and Peek, R. M., Jr.},
   title = {Pathobiology of Helicobacter pylori-Induced Gastric Cancer},
   journal = {Gastroenterology},
   volume = {150},
   number = {1},
   pages = {64-78},
   ISSN = {1528-0012 (Electronic)
0016-5085 (Linking)},
   DOI = {10.1053/j.gastro.2015.09.004},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/26385073},
   year = {2016},
   type = {Journal Article}
}

@article{RN4065,
   author = {Andersson, A. F. and Lindberg, M. and Jakobsson, H. and Backhed, F. and Nyren, P. and Engstrand, L.},
   title = {Comparative analysis of human gut microbiota by barcoded pyrosequencing},
   journal = {PLoS One},
   volume = {3},
   number = {7},
   pages = {e2836},
   ISSN = {1932-6203 (Electronic)
1932-6203 (Linking)},
   DOI = {10.1371/journal.pone.0002836},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/18665274},
   year = {2008},
   type = {Journal Article}
}

@article{RN4194,
   author = {Arumugam, M. and Raes, J. and Pelletier, E. and Le Paslier, D. and Yamada, T. and Mende, D. R. and Fernandes, G. R. and Tap, J. and Bruls, T. and Batto, J. M. and Bertalan, M. and Borruel, N. and Casellas, F. and Fernandez, L. and Gautier, L. and Hansen, T. and Hattori, M. and Hayashi, T. and Kleerebezem, M. and Kurokawa, K. and Leclerc, M. and Levenez, F. and Manichanh, C. and Nielsen, H. B. and Nielsen, T. and Pons, N. and Poulain, J. and Qin, J. and Sicheritz-Ponten, T. and Tims, S. and Torrents, D. and Ugarte, E. and Zoetendal, E. G. and Wang, J. and Guarner, F. and Pedersen, O. and de Vos, W. M. and Brunak, S. and Dore, J. and Meta, H. I. T. Consortium and Antolin, M. and Artiguenave, F. and Blottiere, H. M. and Almeida, M. and Brechot, C. and Cara, C. and Chervaux, C. and Cultrone, A. and Delorme, C. and Denariaz, G. and Dervyn, R. and Foerstner, K. U. and Friss, C. and van de Guchte, M. and Guedon, E. and Haimet, F. and Huber, W. and van Hylckama-Vlieg, J. and Jamet, A. and Juste, C. and Kaci, G. and Knol, J. and Lakhdari, O. and Layec, S. and Le Roux, K. and Maguin, E. and Merieux, A. and Melo Minardi, R. and M'Rini, C. and Muller, J. and Oozeer, R. and Parkhill, J. and Renault, P. and Rescigno, M. and Sanchez, N. and Sunagawa, S. and Torrejon, A. and Turner, K. and Vandemeulebrouck, G. and Varela, E. and Winogradsky, Y. and Zeller, G. and Weissenbach, J. and Ehrlich, S. D. and Bork, P.},
   title = {Enterotypes of the human gut microbiome},
   journal = {Nature},
   volume = {473},
   number = {7346},
   pages = {174-80},
   ISSN = {1476-4687 (Electronic)
0028-0836 (Linking)},
   DOI = {10.1038/nature09944},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/21508958},
   year = {2011},
   type = {Journal Article}
}

@article{RN4115,
   author = {Azad, M. B. and Konya, T. and Maughan, H. and Guttman, D. S. and Field, C. J. and Chari, R. S. and Sears, M. R. and Becker, A. B. and Scott, J. A. and Kozyrskyj, A. L. and Investigators, Child Study},
   title = {Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months},
   journal = {CMAJ},
   volume = {185},
   number = {5},
   pages = {385-94},
   ISSN = {1488-2329 (Electronic)
0820-3946 (Linking)},
   DOI = {10.1503/cmaj.121189},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/23401405},
   year = {2013},
   type = {Journal Article}
}

@article{RN4131,
   author = {Bashan, A. and Gibson, T. E. and Friedman, J. and Carey, V. J. and Weiss, S. T. and Hohmann, E. L. and Liu, Y. Y.},
   title = {Universality of human microbial dynamics},
   journal = {Nature},
   volume = {534},
   number = {7606},
   pages = {259-62},
   ISSN = {1476-4687 (Electronic)
0028-0836 (Linking)},
   DOI = {10.1038/nature18301},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27279224},
   year = {2016},
   type = {Journal Article}
}

@article{RN4144,
   author = {Bjorkholm, B. and Bok, C. M. and Lundin, A. and Rafter, J. and Hibberd, M. L. and Pettersson, S.},
   title = {Intestinal microbiota regulate xenobiotic metabolism in the liver},
   journal = {PLoS One},
   volume = {4},
   number = {9},
   pages = {e6958},
   ISSN = {1932-6203 (Electronic)
1932-6203 (Linking)},
   DOI = {10.1371/journal.pone.0006958},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/19742318},
   year = {2009},
   type = {Journal Article}
}

@article{RN4098,
   author = {Blair, J. M. and Webber, M. A. and Baylay, A. J. and Ogbolu, D. O. and Piddock, L. J.},
   title = {Molecular mechanisms of antibiotic resistance},
   journal = {Nat Rev Microbiol},
   volume = {13},
   number = {1},
   pages = {42-51},
   ISSN = {1740-1534 (Electronic)
1740-1526 (Linking)},
   DOI = {10.1038/nrmicro3380},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/25435309},
   year = {2015},
   type = {Journal Article}
}

@article{RN4079,
   author = {Blaser, M. J. and Falkow, S.},
   title = {What are the consequences of the disappearing human microbiota?},
   journal = {Nat Rev Microbiol},
   volume = {7},
   number = {12},
   pages = {887-94},
   ISSN = {1740-1534 (Electronic)
1740-1526 (Linking)},
   DOI = {10.1038/nrmicro2245},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/19898491},
   year = {2009},
   type = {Journal Article}
}

@article{RN4160,
   author = {Bokulich, N. A. and Subramanian, S. and Faith, J. J. and Gevers, D. and Gordon, J. I. and Knight, R. and Mills, D. A. and Caporaso, J. G.},
   title = {Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing},
   journal = {Nat Methods},
   volume = {10},
   number = {1},
   pages = {57-9},
   ISSN = {1548-7105 (Electronic)
1548-7091 (Linking)},
   DOI = {10.1038/nmeth.2276},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/23202435},
   year = {2013},
   type = {Journal Article}
}

@article{RN4046,
   author = {Browne, H. P. and Forster, S. C. and Anonye, B. O. and Kumar, N. and Neville, B. A. and Stares, M. D. and Goulding, D. and Lawley, T. D.},
   title = {Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation},
   journal = {Nature},
   volume = {533},
   number = {7604},
   pages = {543-6},
   ISSN = {1476-4687 (Electronic)
0028-0836 (Linking)},
   DOI = {10.1038/nature17645},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27144353},
   year = {2016},
   type = {Journal Article}
}

@article{RN4116,
   author = {Chu, D. M. and Ma, J. and Prince, A. L. and Antony, K. M. and Seferovic, M. D. and Aagaard, K. M.},
   title = {Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery},
   journal = {Nat Med},
   volume = {23},
   number = {3},
   pages = {314-326},
   ISSN = {1546-170X (Electronic)
1078-8956 (Linking)},
   DOI = {10.1038/nm.4272},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28112736},
   year = {2017},
   type = {Journal Article}
}

@article{RN4058,
   author = {Clauset, A. and Larremore, D. B. and Sinatra, R.},
   title = {Data-driven predictions in the science of science},
   journal = {Science},
   volume = {355},
   number = {6324},
   pages = {477-480},
   ISSN = {1095-9203 (Electronic)
0036-8075 (Linking)},
   DOI = {10.1126/science.aal4217},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28154048},
   year = {2017},
   type = {Journal Article}
}

@article{RN4111,
   author = {Clemente, J. C. and Pehrsson, E. C. and Blaser, M. J. and Sandhu, K. and Gao, Z. and Wang, B. and Magris, M. and Hidalgo, G. and Contreras, M. and Noya-Alarcon, O. and Lander, O. and McDonald, J. and Cox, M. and Walter, J. and Oh, P. L. and Ruiz, J. F. and Rodriguez, S. and Shen, N. and Song, S. J. and Metcalf, J. and Knight, R. and Dantas, G. and Dominguez-Bello, M. G.},
   title = {The microbiome of uncontacted Amerindians},
   journal = {Sci Adv},
   volume = {1},
   number = {3},
   ISSN = {2375-2548 (Linking)},
   DOI = {10.1126/sciadv.1500183},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/26229982},
   year = {2015},
   type = {Journal Article}
}

@misc{RN4108,
   title = {The American Gut Project},
   howpublished={\url{http://americangut.org/}},
   url = {http://americangut.org/},
   year = {2017},
   type = {Web Page}
}

@article{RN4057,
   author = {Debelius, J. and Song, S. J. and Vazquez-Baeza, Y. and Xu, Z. Z. and Gonzalez, A. and Knight, R.},
   title = {Tiny microbes, enormous impacts: what matters in gut microbiome studies?},
   journal = {Genome Biol},
   volume = {17},
   number = {1},
   pages = {217},
   ISSN = {1474-760X (Electronic)
1474-7596 (Linking)},
   DOI = {10.1186/s13059-016-1086-x},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27760558},
   year = {2016},
   type = {Journal Article}
}

@article{RN4163,
   author = {Dhariwal, A. and Chong, J. and Habib, S. and King, I. L. and Agellon, L. B. and Xia, J.},
   title = {MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data},
   journal = {Nucleic Acids Res},
   ISSN = {1362-4962 (Electronic)
0305-1048 (Linking)},
   DOI = {10.1093/nar/gkx295},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28449106},
   year = {2017},
   type = {Journal Article}
}

@article{RN4140,
   author = {Diaz Heijtz, R. and Wang, S. and Anuar, F. and Qian, Y. and Bjorkholm, B. and Samuelsson, A. and Hibberd, M. L. and Forssberg, H. and Pettersson, S.},
   title = {Normal gut microbiota modulates brain development and behavior},
   journal = {Proc Natl Acad Sci U S A},
   volume = {108},
   number = {7},
   pages = {3047-52},
   ISSN = {1091-6490 (Electronic)
0027-8424 (Linking)},
   DOI = {10.1073/pnas.1010529108},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/21282636},
   year = {2011},
   type = {Journal Article}
}

@article{RN4118,
   author = {Dominguez-Bello, M. G. and Costello, E. K. and Contreras, M. and Magris, M. and Hidalgo, G. and Fierer, N. and Knight, R.},
   title = {Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns},
   journal = {Proc Natl Acad Sci U S A},
   volume = {107},
   number = {26},
   pages = {11971-5},
   ISSN = {1091-6490 (Electronic)
0027-8424 (Linking)},
   DOI = {10.1073/pnas.1002601107},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/20566857},
   year = {2010},
   type = {Journal Article}
}

@article{RN4271,
   author = {Fierer, N. and Lauber, C. L. and Zhou, N. and McDonald, D. and Costello, E. K. and Knight, R.},
   title = {Forensic identification using skin bacterial communities},
   journal = {Proc Natl Acad Sci U S A},
   volume = {107},
   number = {14},
   pages = {6477-81},
   ISSN = {1091-6490 (Electronic)
0027-8424 (Linking)},
   DOI = {10.1073/pnas.1000162107},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/20231444},
   year = {2010},
   type = {Journal Article}
}

@article{RN4083,
   author = {Dunn, R. R. and Fierer, N. and Henley, J. B. and Leff, J. W. and Menninger, H. L.},
   title = {Home life: factors structuring the bacterial diversity found within and between homes},
   journal = {PLoS One},
   volume = {8},
   number = {5},
   pages = {e64133},
   ISSN = {1932-6203 (Electronic)
1932-6203 (Linking)},
   DOI = {10.1371/journal.pone.0064133},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/23717552},
   year = {2013},
   type = {Journal Article}
}

@article{RN4048,
   author = {Eckburg, P. B. and Bik, E. M. and Bernstein, C. N. and Purdom, E. and Dethlefsen, L. and Sargent, M. and Gill, S. R. and Nelson, K. E. and Relman, D. A.},
   title = {Diversity of the human intestinal microbial flora},
   journal = {Science},
   volume = {308},
   number = {5728},
   pages = {1635-8},
   ISSN = {1095-9203 (Electronic)
0036-8075 (Linking)},
   DOI = {10.1126/science.1110591},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/15831718},
   year = {2005},
   type = {Journal Article}
}

@article{RN4086,
   author = {Enright, E. F. and Gahan, C. G. and Joyce, S. A. and Griffin, B. T.},
   title = {The Impact of the Gut Microbiota on Drug Metabolism and Clinical Outcome},
   journal = {Yale J Biol Med},
   volume = {89},
   number = {3},
   pages = {375-382},
   ISSN = {1551-4056 (Electronic)
0044-0086 (Linking)},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27698621},
   year = {2016},
   type = {Journal Article}
}

@article{RN4104,
   author = {Falony, G. and Joossens, M. and Vieira-Silva, S. and Wang, J. and Darzi, Y. and Faust, K. and Kurilshikov, A. and Bonder, M. J. and Valles-Colomer, M. and Vandeputte, D. and Tito, R. Y. and Chaffron, S. and Rymenans, L. and Verspecht, C. and De Sutter, L. and Lima-Mendez, G. and D'Hoe, K. and Jonckheere, K. and Homola, D. and Garcia, R. and Tigchelaar, E. F. and Eeckhaudt, L. and Fu, J. and Henckaerts, L. and Zhernakova, A. and Wijmenga, C. and Raes, J.},
   title = {Population-level analysis of gut microbiome variation},
   journal = {Science},
   volume = {352},
   number = {6285},
   pages = {560-4},
   ISSN = {1095-9203 (Electronic)
0036-8075 (Linking)},
   DOI = {10.1126/science.aad3503},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27126039},
   year = {2016},
   type = {Journal Article}
}

@article{RN4148,
   author = {Faustino, C. and Serafim, C. and Rijo, P. and Reis, C. P.},
   title = {Bile acids and bile acid derivatives: use in drug delivery systems and as therapeutic agents},
   journal = {Expert Opin Drug Deliv},
   volume = {13},
   number = {8},
   pages = {1133-48},
   ISSN = {1744-7593 (Electronic)
1742-5247 (Linking)},
   DOI = {10.1080/17425247.2016.1178233},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27102882},
   year = {2016},
   type = {Journal Article}
}

@article{RN4101,
   author = {Garcia-Gonzalez, A. P. and Ritter, A. D. and Shrestha, S. and Andersen, E. C. and Yilmaz, L. S. and Walhout, A. J. M.},
   title = {Bacterial Metabolism Affects the C. elegans Response to Cancer Chemotherapeutics},
   journal = {Cell},
   volume = {169},
   number = {3},
   pages = {431-441 e8},
   ISSN = {1097-4172 (Electronic)
0092-8674 (Linking)},
   DOI = {10.1016/j.cell.2017.03.046},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28431244},
   year = {2017},
   type = {Journal Article}
}

@article{RN4080,
   author = {Gilbert, J. A. and Quinn, R. A. and Debelius, J. and Xu, Z. Z. and Morton, J. and Garg, N. and Jansson, J. K. and Dorrestein, P. C. and Knight, R.},
   title = {Microbiome-wide association studies link dynamic microbial consortia to disease},
   journal = {Nature},
   volume = {535},
   number = {7610},
   pages = {94-103},
   ISSN = {1476-4687 (Electronic)
0028-0836 (Linking)},
   DOI = {10.1038/nature18850},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27383984},
   year = {2016},
   type = {Journal Article}
}

@article{RN4055,
   author = {Gill, S. R. and Pop, M. and Deboy, R. T. and Eckburg, P. B. and Turnbaugh, P. J. and Samuel, B. S. and Gordon, J. I. and Relman, D. A. and Fraser-Liggett, C. M. and Nelson, K. E.},
   title = {Metagenomic analysis of the human distal gut microbiome},
   journal = {Science},
   volume = {312},
   number = {5778},
   pages = {1355-9},
   ISSN = {1095-9203 (Electronic)
0036-8075 (Linking)},
   DOI = {10.1126/science.1124234},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/16741115},
   year = {2006},
   type = {Journal Article}
}

@article{RN4162,
   author = {Glass, E. M. and Wilkening, J. and Wilke, A. and Antonopoulos, D. and Meyer, F.},
   title = {Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes},
   journal = {Cold Spring Harb Protoc},
   volume = {2010},
   number = {1},
   pages = {pdb prot5368},
   ISSN = {1559-6095 (Electronic)
1559-6095 (Linking)},
   DOI = {10.1101/pdb.prot5368},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/20150127},
   year = {2010},
   type = {Journal Article}
}

@article{RN4102,
   author = {Haiser, H. J. and Gootenberg, D. B. and Chatman, K. and Sirasani, G. and Balskus, E. P. and Turnbaugh, P. J.},
   title = {Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta},
   journal = {Science},
   volume = {341},
   number = {6143},
   pages = {295-8},
   ISSN = {1095-9203 (Electronic)
0036-8075 (Linking)},
   DOI = {10.1126/science.1235872},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/23869020},
   year = {2013},
   type = {Journal Article}
}

@article{RN4146,
   author = {Haiser, H. J. and Seim, K. L. and Balskus, E. P. and Turnbaugh, P. J.},
   title = {Mechanistic insight into digoxin inactivation by Eggerthella lenta augments our understanding of its pharmacokinetics},
   journal = {Gut Microbes},
   volume = {5},
   number = {2},
   pages = {233-8},
   ISSN = {1949-0984 (Electronic)
1949-0976 (Linking)},
   DOI = {10.4161/gmic.27915},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/24637603},
   year = {2014},
   type = {Journal Article}
}

@article{RN4081,
   author = {Hamady, M. and Knight, R.},
   title = {Microbial community profiling for human microbiome projects: Tools, techniques, and challenges},
   journal = {Genome Res},
   volume = {19},
   number = {7},
   pages = {1141-52},
   ISSN = {1088-9051 (Print)
1088-9051 (Linking)},
   DOI = {10.1101/gr.085464.108},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/19383763},
   year = {2009},
   type = {Journal Article}
}

@article{RN4056,
   author = {Hamady, M. and Walker, J. J. and Harris, J. K. and Gold, N. J. and Knight, R.},
   title = {Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex},
   journal = {Nat Methods},
   volume = {5},
   number = {3},
   pages = {235-7},
   ISSN = {1548-7105 (Electronic)
1548-7091 (Linking)},
   DOI = {10.1038/nmeth.1184},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/18264105},
   year = {2008},
   type = {Journal Article}
}

@article{RN4180,
   author = {Hill-Burns, E. M. and Debelius, J. W. and Morton, J. T. and Wissemann, W. T. and Lewis, M. R. and Wallen, Z. D. and Peddada, S. D. and Factor, S. A. and Molho, E. and Zabetian, C. P. and Knight, R. and Payami, H.},
   title = {Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome},
   journal = {Mov Disord},
   volume = {32},
   number = {5},
   pages = {739-749},
   ISSN = {1531-8257 (Electronic)
0885-3185 (Linking)},
   DOI = {10.1002/mds.26942},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28195358},
   year = {2017},
   type = {Journal Article}
}

@article{RN4139,
   author = {Hullar, M. A. and Burnett-Hartman, A. N. and Lampe, J. W.},
   title = {Gut microbes, diet, and cancer},
   journal = {Cancer Treat Res},
   volume = {159},
   pages = {377-99},
   ISSN = {0927-3042 (Print)
0927-3042 (Linking)},
   DOI = {10.1007/978-3-642-38007-5_22},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/24114492},
   year = {2014},
   type = {Journal Article}
}

@article{RN4164,
   author = {Huse, S. M. and Mark Welch, D. B. and Voorhis, A. and Shipunova, A. and Morrison, H. G. and Eren, A. M. and Sogin, M. L.},
   title = {VAMPS: a website for visualization and analysis of microbial population structures},
   journal = {BMC Bioinformatics},
   volume = {15},
   pages = {41},
   ISSN = {1471-2105 (Electronic)
1471-2105 (Linking)},
   DOI = {10.1186/1471-2105-15-41},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/24499292},
   year = {2014},
   type = {Journal Article}
}

@article{RN4134,
   author = {Ishikawa, D. and Sasaki, T. and Osada, T. and Kuwahara-Arai, K. and Haga, K. and Shibuya, T. and Hiramatsu, K. and Watanabe, S.},
   title = {Changes in Intestinal Microbiota Following Combination Therapy with Fecal Microbial Transplantation and Antibiotics for Ulcerative Colitis},
   journal = {Inflamm Bowel Dis},
   volume = {23},
   number = {1},
   pages = {116-125},
   ISSN = {1536-4844 (Electronic)
1078-0998 (Linking)},
   DOI = {10.1097/MIB.0000000000000975},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27893543},
   year = {2017},
   type = {Journal Article}
}

@article{RN4175,
   author = {Jacobs, J. P. and Goudarzi, M. and Singh, N. and Tong, M. and McHardy, I. H. and Ruegger, P. and Asadourian, M. and Moon, B. H. and Ayson, A. and Borneman, J. and McGovern, D. P. and Fornace, A. J., Jr. and Braun, J. and Dubinsky, M.},
   title = {A Disease-Associated Microbial and Metabolomics State in Relatives of Pediatric Inflammatory Bowel Disease Patients},
   journal = {Cell Mol Gastroenterol Hepatol},
   volume = {2},
   number = {6},
   pages = {750-766},
   ISSN = {2352-345X (Linking)},
   DOI = {10.1016/j.jcmgh.2016.06.004},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28174747},
   year = {2016},
   type = {Journal Article}
}

@article{RN4143,
   author = {Kelly, S. L. and Kelly, D. E.},
   title = {Microbial cytochromes P450: biodiversity and biotechnology. Where do cytochromes P450 come from, what do they do and what can they do for us?},
   journal = {Philos Trans R Soc Lond B Biol Sci},
   volume = {368},
   number = {1612},
   pages = {20120476},
   ISSN = {1471-2970 (Electronic)
0962-8436 (Linking)},
   DOI = {10.1098/rstb.2012.0476},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/23297358},
   year = {2013},
   type = {Journal Article}
}

@article{RN4133,
   author = {Keshteli, A. H. and Millan, B. and Madsen, K. L.},
   title = {Pretreatment with antibiotics may enhance the efficacy of fecal microbiota transplantation in ulcerative colitis: a meta-analysis},
   journal = {Mucosal Immunol},
   volume = {10},
   number = {2},
   pages = {565-566},
   ISSN = {1935-3456 (Electronic)
1933-0219 (Linking)},
   DOI = {10.1038/mi.2016.123},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28000680},
   year = {2017},
   type = {Journal Article}
}

@article{RN4054,
   author = {Kim, D. and Song, L. and Breitwieser, F. P. and Salzberg, S. L.},
   title = {Centrifuge: rapid and sensitive classification of metagenomic sequences},
   journal = {Genome Res},
   volume = {26},
   number = {12},
   pages = {1721-1729},
   ISSN = {1549-5469 (Electronic)
1088-9051 (Linking)},
   DOI = {10.1101/gr.210641.116},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27852649},
   year = {2016},
   type = {Journal Article}
}

@article{RN4090,
   author = {Kim, I. S. and Yoo, D. H. and Jung, I. H. and Lim, S. and Jeong, J. J. and Kim, K. A. and Bae, O. N. and Yoo, H. H. and Kim, D. H.},
   title = {Reduced metabolic activity of gut microbiota by antibiotics can potentiate the antithrombotic effect of aspirin},
   journal = {Biochem Pharmacol},
   volume = {122},
   pages = {72-79},
   ISSN = {1873-2968 (Electronic)
0006-2952 (Linking)},
   DOI = {10.1016/j.bcp.2016.09.023},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27687643},
   year = {2016},
   type = {Journal Article}
}

@article{RN4126,
   author = {Kirpichnikov, D. and McFarlane, S. I. and Sowers, J. R.},
   title = {Metformin: an update},
   journal = {Ann Intern Med},
   volume = {137},
   number = {1},
   pages = {25-33},
   ISSN = {1539-3704 (Electronic)
0003-4819 (Linking)},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/12093242},
   year = {2002},
   type = {Journal Article}
}

@article{RN4195,
   author = {Knights, D. and Ward, T. L. and McKinlay, C. E. and Miller, H. and Gonzalez, A. and McDonald, D. and Knight, R.},
   title = {Rethinking ``enterotype''},
   journal = {Cell Host Microbe},
   volume = {16},
   number = {4},
   pages = {433-7},
   ISSN = {1934-6069 (Electronic)
1931-3128 (Linking)},
   DOI = {10.1016/j.chom.2014.09.013},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/25299329},
   year = {2014},
   type = {Journal Article}
}

@article{RN4177,
   author = {Konikoff, M. R. and Denson, L. A.},
   title = {Role of fecal calprotectin as a biomarker of intestinal inflammation in inflammatory bowel disease},
   journal = {Inflamm Bowel Dis},
   volume = {12},
   number = {6},
   pages = {524-34},
   ISSN = {1078-0998 (Print)
1078-0998 (Linking)},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/16775498},
   year = {2006},
   type = {Journal Article}
}

@article{RN4193,
   author = {Korem, T. and Zeevi, D. and Zmora, N. and Weissbrod, O. and Bar, N. and Lotan-Pompan, M. and Avnit-Sagi, T. and Kosower, N. and Malka, G. and Rein, M. and Suez, J. and Goldberg, B. Z. and Weinberger, A. and Levy, A. A. and Elinav, E. and Segal, E.},
   title = {Bread Affects Clinical Parameters and Induces Gut Microbiome-Associated Personal Glycemic Responses},
   journal = {Cell Metab},
   volume = {25},
   number = {6},
   pages = {1243-1253 e5},
   ISSN = {1932-7420 (Electronic)
1550-4131 (Linking)},
   DOI = {10.1016/j.cmet.2017.05.002},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28591632},
   year = {2017},
   type = {Journal Article}
}

@article{RN4196,
   author = {Koren, O. and Knights, D. and Gonzalez, A. and Waldron, L. and Segata, N. and Knight, R. and Huttenhower, C. and Ley, R. E.},
   title = {A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets},
   journal = {PLoS Comput Biol},
   volume = {9},
   number = {1},
   pages = {e1002863},
   ISSN = {1553-7358 (Electronic)
1553-734X (Linking)},
   DOI = {10.1371/journal.pcbi.1002863},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/23326225},
   year = {2013},
   type = {Journal Article}
}

@article{RN4156,
   author = {Kurdi, P. and Tanaka, H. and Van Veen, H. W. and Asano, K. and Tomita, F. and Yokota, A.},
   title = {Cholic acid accumulation and its diminution by short-chain fatty acids in bifidobacteria},
   journal = {Microbiology},
   volume = {149},
   number = {Pt 8},
   pages = {2031-7},
   ISSN = {1350-0872 (Print)
1350-0872 (Linking)},
   DOI = {10.1099/mic.0.26376-0},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/12904543},
   year = {2003},
   type = {Journal Article}
}

@article{RN4186,
   author = {Kurtz, Z. D. and Muller, C. L. and Miraldi, E. R. and Littman, D. R. and Blaser, M. J. and Bonneau, R. A.},
   title = {Sparse and compositionally robust inference of microbial ecological networks},
   journal = {PLoS Comput Biol},
   volume = {11},
   number = {5},
   pages = {e1004226},
   ISSN = {1553-7358 (Electronic)
1553-734X (Linking)},
   DOI = {10.1371/journal.pcbi.1004226},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/25950956},
   year = {2015},
   type = {Journal Article}
}

@article{RN4043,
   author = {Lander, E. S. and Linton, L. M. and Birren, B. and Nusbaum, C. and Zody, M. C. and Baldwin, J. and Devon, K. and Dewar, K. and Doyle, M. and FitzHugh, W. and Funke, R. and Gage, D. and Harris, K. and Heaford, A. and Howland, J. and Kann, L. and Lehoczky, J. and LeVine, R. and McEwan, P. and McKernan, K. and Meldrim, J. and Mesirov, J. P. and Miranda, C. and Morris, W. and Naylor, J. and Raymond, C. and Rosetti, M. and Santos, R. and Sheridan, A. and Sougnez, C. and Stange-Thomann, Y. and Stojanovic, N. and Subramanian, A. and Wyman, D. and Rogers, J. and Sulston, J. and Ainscough, R. and Beck, S. and Bentley, D. and Burton, J. and Clee, C. and Carter, N. and Coulson, A. and Deadman, R. and Deloukas, P. and Dunham, A. and Dunham, I. and Durbin, R. and French, L. and Grafham, D. and Gregory, S. and Hubbard, T. and Humphray, S. and Hunt, A. and Jones, M. and Lloyd, C. and McMurray, A. and Matthews, L. and Mercer, S. and Milne, S. and Mullikin, J. C. and Mungall, A. and Plumb, R. and Ross, M. and Shownkeen, R. and Sims, S. and Waterston, R. H. and Wilson, R. K. and Hillier, L. W. and McPherson, J. D. and Marra, M. A. and Mardis, E. R. and Fulton, L. A. and Chinwalla, A. T. and Pepin, K. H. and Gish, W. R. and Chissoe, S. L. and Wendl, M. C. and Delehaunty, K. D. and Miner, T. L. and Delehaunty, A. and Kramer, J. B. and Cook, L. L. and Fulton, R. S. and Johnson, D. L. and Minx, P. J. and Clifton, S. W. and Hawkins, T. and Branscomb, E. and Predki, P. and Richardson, P. and Wenning, S. and Slezak, T. and Doggett, N. and Cheng, J. F. and Olsen, A. and Lucas, S. and Elkin, C. and Uberbacher, E. and Frazier, M. and others },
   title = {Initial sequencing and analysis of the human genome},
   journal = {Nature},
   volume = {409},
   number = {6822},
   pages = {860-921},
   ISSN = {0028-0836 (Print)
0028-0836 (Linking)},
   DOI = {10.1038/35057062},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/11237011},
   year = {2001},
   type = {Journal Article}
}

@article{RN4087,
   author = {Ley, R. E. and Lozupone, C. A. and Hamady, M. and Knight, R. and Gordon, J. I.},
   title = {Worlds within worlds: evolution of the vertebrate gut microbiota},
   journal = {Nat Rev Microbiol},
   volume = {6},
   number = {10},
   pages = {776-88},
   ISSN = {1740-1534 (Electronic)
1740-1526 (Linking)},
   DOI = {10.1038/nrmicro1978},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/18794915},
   year = {2008},
   type = {Journal Article}
}

@article{RN4099,
   author = {Lindenbaum, J. and Rund, D. G. and Butler, V. P., Jr. and Tse-Eng, D. and Saha, J. R.},
   title = {Inactivation of digoxin by the gut flora: reversal by antibiotic therapy},
   journal = {N Engl J Med},
   volume = {305},
   number = {14},
   pages = {789-94},
   ISSN = {0028-4793 (Print)
0028-4793 (Linking)},
   DOI = {10.1056/NEJM198110013051403},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/7266632},
   year = {1981},
   type = {Journal Article}
}

@article{RN4202,
   author = {Lu, L. and Wu, Y. and Zuo, L. and Luo, X. and Large, P. J.},
   title = {Intestinal microbiome and digoxin inactivation: meal plan for digoxin users?},
   journal = {World J Microbiol Biotechnol},
   volume = {30},
   number = {3},
   pages = {791-9},
   ISSN = {1573-0972 (Electronic)
0959-3993 (Linking)},
   DOI = {10.1007/s11274-013-1507-x},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/24105082},
   year = {2014},
   type = {Journal Article}
}

@article{RN4141,
   author = {Lupton, J. R.},
   title = {Microbial degradation products influence colon cancer risk: the butyrate controversy},
   journal = {J Nutr},
   volume = {134},
   number = {2},
   pages = {479-82},
   ISSN = {0022-3166 (Print)
0022-3166 (Linking)},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/14747692},
   year = {2004},
   type = {Journal Article}
}

@article{RN4153,
   author = {Magee, E. A. and Richardson, C. J. and Hughes, R. and Cummings, J. H.},
   title = {Contribution of dietary protein to sulfide production in the large intestine: an in vitro and a controlled feeding study in humans},
   journal = {Am J Clin Nutr},
   volume = {72},
   number = {6},
   pages = {1488-94},
   ISSN = {0002-9165 (Print)
0002-9165 (Linking)},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/11101476},
   year = {2000},
   type = {Journal Article}
}

@article{RN4110,
   author = {Marteau, P. and Pochart, P. and Dore, J. and Bera-Maillet, C. and Bernalier, A. and Corthier, G.},
   title = {Comparative study of bacterial groups within the human cecal and fecal microbiota},
   journal = {Appl Environ Microbiol},
   volume = {67},
   number = {10},
   pages = {4939-42},
   ISSN = {0099-2240 (Print)
0099-2240 (Linking)},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/11571208},
   year = {2001},
   type = {Journal Article}
}

@article{RN4138,
   author = {Martz, S. L. and Guzman-Rodriguez, M. and He, S. M. and Noordhof, C. and Hurlbut, D. J. and Gloor, G. B. and Carlucci, C. and Weese, S. and Allen-Vercoe, E. and Sun, J. and Claud, E. C. and Petrof, E. O.},
   title = {A human gut ecosystem protects against C. difficile disease by targeting TcdA},
   journal = {J Gastroenterol},
   volume = {52},
   number = {4},
   pages = {452-465},
   ISSN = {1435-5922 (Electronic)
0944-1174 (Linking)},
   DOI = {10.1007/s00535-016-1232-y},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27329502},
   year = {2017},
   type = {Journal Article}
}

@article{RN4103,
   author = {Maruthur, N. M. and Tseng, E. and Hutfless, S. and Wilson, L. M. and Suarez-Cuervo, C. and Berger, Z. and Chu, Y. and Iyoha, E. and Segal, J. B. and Bolen, S.},
   title = {Diabetes Medications as Monotherapy or Metformin-Based Combination Therapy for Type 2 Diabetes: A Systematic Review and Meta-analysis},
   journal = {Ann Intern Med},
   volume = {164},
   number = {11},
   pages = {740-51},
   ISSN = {1539-3704 (Electronic)
0003-4819 (Linking)},
   DOI = {10.7326/M15-2650},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27088241},
   year = {2016},
   type = {Journal Article}
}

@article{RN4147,
   author = {Mataki, C. and Magnier, B. C. and Houten, S. M. and Annicotte, J. S. and Argmann, C. and Thomas, C. and Overmars, H. and Kulik, W. and Metzger, D. and Auwerx, J. and Schoonjans, K.},
   title = {Compromised intestinal lipid absorption in mice with a liver-specific deficiency of liver receptor homolog 1},
   journal = {Mol Cell Biol},
   volume = {27},
   number = {23},
   pages = {8330-9},
   ISSN = {1098-5549 (Electronic)
0270-7306 (Linking)},
   DOI = {10.1128/MCB.00852-07},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/17908794},
   year = {2007},
   type = {Journal Article}
}

@article{RN4201,
   author = {Matuskova, Z. and Anzenbacherova, E. and Vecera, R. and Tlaskalova-Hogenova, H. and Kolar, M. and Anzenbacher, P.},
   title = {Administration of a probiotic can change drug pharmacokinetics: effect of E. coli Nissle 1917 on amidarone absorption in rats},
   journal = {PLoS One},
   volume = {9},
   number = {2},
   pages = {e87150},
   ISSN = {1932-6203 (Electronic)
1932-6203 (Linking)},
   DOI = {10.1371/journal.pone.0087150},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/24505278},
   year = {2014},
   type = {Journal Article}
}

@article{RN4095,
   author = {Maurice, C. F. and Haiser, H. J. and Turnbaugh, P. J.},
   title = {Xenobiotics shape the physiology and gene expression of the active human gut microbiome},
   journal = {Cell},
   volume = {152},
   number = {1-2},
   pages = {39-50},
   ISSN = {1097-4172 (Electronic)
0092-8674 (Linking)},
   DOI = {10.1016/j.cell.2012.10.052},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/23332745},
   year = {2013},
   type = {Journal Article}
}

@article{RN4128,
   author = {McCreight, L. J. and Bailey, C. J. and Pearson, E. R.},
   title = {Metformin and the gastrointestinal tract},
   journal = {Diabetologia},
   volume = {59},
   number = {3},
   pages = {426-35},
   ISSN = {1432-0428 (Electronic)
0012-186X (Linking)},
   DOI = {10.1007/s00125-015-3844-9},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/26780750},
   year = {2016},
   type = {Journal Article}
}

@article{RN4152,
   author = {McGarr, S. E. and Ridlon, J. M. and Hylemon, P. B.},
   title = {Diet, anaerobic bacterial metabolism, and colon cancer: a review of the literature},
   journal = {J Clin Gastroenterol},
   volume = {39},
   number = {2},
   pages = {98-109},
   ISSN = {0192-0790 (Print)
0192-0790 (Linking)},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/15681903},
   year = {2005},
   type = {Journal Article}
}

@article{RN4135,
   author = {Nakatsuji, T. and Chen, T. H. and Narala, S. and Chun, K. A. and Two, A. M. and Yun, T. and Shafiq, F. and Kotol, P. F. and Bouslimani, A. and Melnik, A. V. and Latif, H. and Kim, J. N. and Lockhart, A. and Artis, K. and David, G. and Taylor, P. and Streib, J. and Dorrestein, P. C. and Grier, A. and Gill, S. R. and Zengler, K. and Hata, T. R. and Leung, D. Y. and Gallo, R. L.},
   title = {Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis},
   journal = {Sci Transl Med},
   volume = {9},
   number = {378},
   ISSN = {1946-6242 (Electronic)
1946-6234 (Linking)},
   DOI = {10.1126/scitranslmed.aah4680},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28228596},
   year = {2017},
   type = {Journal Article}
}

@article{RN4096,
   author = {Novo, D. J. and Perlmutter, N. G. and Hunt, R. H. and Shapiro, H. M.},
   title = {Multiparameter flow cytometric analysis of antibiotic effects on membrane potential, membrane permeability, and bacterial counts of Staphylococcus aureus and Micrococcus luteus},
   journal = {Antimicrob Agents Chemother},
   volume = {44},
   number = {4},
   pages = {827-34},
   ISSN = {0066-4804 (Print)
0066-4804 (Linking)},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/10722477},
   year = {2000},
   type = {Journal Article}
}

@article{RN4053,
   author = {Nurk, S. and Meleshko, D. and Korobeynikov, A. and Pevzner, P. A.},
   title = {metaSPAdes: a new versatile metagenomic assembler},
   journal = {Genome Res},
   volume = {27},
   number = {5},
   pages = {824-834},
   ISSN = {1549-5469 (Electronic)
1088-9051 (Linking)},
   DOI = {10.1101/gr.213959.116},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28298430},
   year = {2017},
   type = {Journal Article}
}

@article{RN4109,
   author = {Otani, K. and Tanigawa, T. and Watanabe, T. and Shimada, S. and Nadatani, Y. and Nagami, Y. and Tanaka, F. and Kamata, N. and Yamagami, H. and Shiba, M. and Tominaga, K. and Fujiwara, Y. and Arakawa, T.},
   title = {Microbiota Plays a Key Role in Non-Steroidal Anti-Inflammatory Drug-Induced Small Intestinal Damage},
   journal = {Digestion},
   volume = {95},
   number = {1},
   pages = {22-28},
   ISSN = {1421-9867 (Electronic)
0012-2823 (Linking)},
   DOI = {10.1159/000452356},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28052268},
   year = {2017},
   type = {Journal Article}
}

@article{RN4047,
   author = {Pace, N. R.},
   title = {A molecular view of microbial diversity and the biosphere},
   journal = {Science},
   volume = {276},
   number = {5313},
   pages = {734-40},
   ISSN = {0036-8075 (Print)
0036-8075 (Linking)},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/9115194},
   year = {1997},
   type = {Journal Article}
}

@article{RN4119,
   author = {Palmer, C. and Bik, E. M. and DiGiulio, D. B. and Relman, D. A. and Brown, P. O.},
   title = {Development of the human infant intestinal microbiota},
   journal = {PLoS Biol},
   volume = {5},
   number = {7},
   pages = {e177},
   ISSN = {1545-7885 (Electronic)
1544-9173 (Linking)},
   DOI = {10.1371/journal.pbio.0050177},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/17594176},
   year = {2007},
   type = {Journal Article}
}

@article{RN4093,
   author = {Peppercorn, M. A. and Goldman, P.},
   title = {The role of intestinal bacteria in the metabolism of salicylazosulfapyridine},
   journal = {J Pharmacol Exp Ther},
   volume = {181},
   number = {3},
   pages = {555-62},
   ISSN = {0022-3565 (Print)
0022-3565 (Linking)},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/4402374},
   year = {1972},
   type = {Journal Article}
}

@article{RN4078,
   author = {Pickrell, J. K. and Pritchard, J. K.},
   title = {Inference of population splits and mixtures from genome-wide allele frequency data},
   journal = {PLoS Genet},
   volume = {8},
   number = {11},
   pages = {e1002967},
   ISSN = {1553-7404 (Electronic)
1553-7390 (Linking)},
   DOI = {10.1371/journal.pgen.1002967},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/23166502},
   year = {2012},
   type = {Journal Article}
}

@article{RN4184,
   author = {Quinn, R. A. and Nothias, L. F. and Vining, O. and Meehan, M. and Esquenazi, E. and Dorrestein, P. C.},
   title = {Molecular Networking As a Drug Discovery, Drug Metabolism, and Precision Medicine Strategy},
   journal = {Trends Pharmacol Sci},
   volume = {38},
   number = {2},
   pages = {143-154},
   ISSN = {1873-3735 (Electronic)
0165-6147 (Linking)},
   DOI = {10.1016/j.tips.2016.10.011},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27842887},
   year = {2017},
   type = {Journal Article}
}

@article{RN4094,
   author = {Rafii, F. and Cerniglia, C. E.},
   title = {Reduction of azo dyes and nitroaromatic compounds by bacterial enzymes from the human intestinal tract},
   journal = {Environ Health Perspect},
   volume = {103 Suppl 5},
   pages = {17-9},
   ISSN = {0091-6765 (Print)
0091-6765 (Linking)},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/8565901},
   year = {1995},
   type = {Journal Article}
}

@article{RN4097,
   author = {Raymond, F. and Ouameur, A. A. and Deraspe, M. and Iqbal, N. and Gingras, H. and Dridi, B. and Leprohon, P. and Plante, P. L. and Giroux, R. and Berube, E. and Frenette, J. and Boudreau, D. K. and Simard, J. L. and Chabot, I. and Domingo, M. C. and Trottier, S. and Boissinot, M. and Huletsky, A. and Roy, P. H. and Ouellette, M. and Bergeron, M. G. and Corbeil, J.},
   title = {The initial state of the human gut microbiome determines its reshaping by antibiotics},
   journal = {ISME J},
   volume = {10},
   number = {3},
   pages = {707-20},
   ISSN = {1751-7370 (Electronic)
1751-7362 (Linking)},
   DOI = {10.1038/ismej.2015.148},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/26359913},
   year = {2016},
   type = {Journal Article}
}

@article{RN4157,
   author = {Reeder, J. and Knight, R.},
   title = {Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions},
   journal = {Nat Methods},
   volume = {7},
   number = {9},
   pages = {668-9},
   ISSN = {1548-7105 (Electronic)
1548-7091 (Linking)},
   DOI = {10.1038/nmeth0910-668b},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/20805793},
   year = {2010},
   type = {Journal Article}
}

@article{RN4149,
   author = {Ridlon, J. M. and Kang, D. J. and Hylemon, P. B.},
   title = {Bile salt biotransformations by human intestinal bacteria},
   journal = {J Lipid Res},
   volume = {47},
   number = {2},
   pages = {241-59},
   ISSN = {0022-2275 (Print)
0022-2275 (Linking)},
   DOI = {10.1194/jlr.R500013-JLR200},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/16299351},
   year = {2006},
   type = {Journal Article}
}

@article{RN4172,
   author = {Sartor, R. B.},
   title = {Microbial influences in inflammatory bowel diseases},
   journal = {Gastroenterology},
   volume = {134},
   number = {2},
   pages = {577-94},
   ISSN = {1528-0012 (Electronic)
0016-5085 (Linking)},
   DOI = {10.1053/j.gastro.2007.11.059},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/18242222},
   year = {2008},
   type = {Journal Article}
}

@article{RN4045,
   author = {Savage, D. C.},
   title = {Microbial ecology of the gastrointestinal tract},
   journal = {Annu Rev Microbiol},
   volume = {31},
   pages = {107-33},
   ISSN = {0066-4227 (Print)
0066-4227 (Linking)},
   DOI = {10.1146/annurev.mi.31.100177.000543},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/334036},
   year = {1977},
   type = {Journal Article}
}

@article{RN4150,
   author = {Sayin, S. I. and Wahlstrom, A. and Felin, J. and Jantti, S. and Marschall, H. U. and Bamberg, K. and Angelin, B. and Hyotylainen, T. and Oresic, M. and Backhed, F.},
   title = {Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist},
   journal = {Cell Metab},
   volume = {17},
   number = {2},
   pages = {225-35},
   ISSN = {1932-7420 (Electronic)
1550-4131 (Linking)},
   DOI = {10.1016/j.cmet.2013.01.003},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/23395169},
   year = {2013},
   type = {Journal Article}
}

@article{RN4085,
   author = {Scarpignato, C. and Dolak, W. and Lanas, A. and Matzneller, P. and Renzulli, C. and Grimaldi, M. and Zeitlinger, M. and Bjarnason, I.},
   title = {Rifaximin Reduces the Number and Severity of Intestinal Lesions Associated With Use of Nonsteroidal Anti-Inflammatory Drugs in Humans},
   journal = {Gastroenterology},
   volume = {152},
   number = {5},
   pages = {980-982 e3},
   ISSN = {1528-0012 (Electronic)
0016-5085 (Linking)},
   DOI = {10.1053/j.gastro.2016.12.007},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28007576},
   year = {2017},
   type = {Journal Article}
}

@article{RN4113,
   author = {Schnorr, S. L. and Candela, M. and Rampelli, S. and Centanni, M. and Consolandi, C. and Basaglia, G. and Turroni, S. and Biagi, E. and Peano, C. and Severgnini, M. and Fiori, J. and Gotti, R. and De Bellis, G. and Luiselli, D. and Brigidi, P. and Mabulla, A. and Marlowe, F. and Henry, A. G. and Crittenden, A. N.},
   title = {Gut microbiome of the Hadza hunter-gatherers},
   journal = {Nat Commun},
   volume = {5},
   pages = {3654},
   ISSN = {2041-1723 (Electronic)
2041-1723 (Linking)},
   DOI = {10.1038/ncomms4654},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/24736369},
   year = {2014},
   type = {Journal Article}
}

@article{RN4100,
   author = {Scott, T. A. and Quintaneiro, L. M. and Norvaisas, P. and Lui, P. P. and Wilson, M. P. and Leung, K. Y. and Herrera-Dominguez, L. and Sudiwala, S. and Pessia, A. and Clayton, P. T. and Bryson, K. and Velagapudi, V. and Mills, P. B. and Typas, A. and Greene, N. D. E. and Cabreiro, F.},
   title = {Host-Microbe Co-metabolism Dictates Cancer Drug Efficacy in C. elegans},
   journal = {Cell},
   volume = {169},
   number = {3},
   pages = {442-456 e18},
   ISSN = {1097-4172 (Electronic)
0092-8674 (Linking)},
   DOI = {10.1016/j.cell.2017.03.040},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28431245},
   year = {2017},
   type = {Journal Article}
}

@article{RN4039,
   author = {Sender, R. and Fuchs, S. and Milo, R.},
   title = {Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans},
   journal = {Cell},
   volume = {164},
   number = {3},
   pages = {337-40},
   ISSN = {1097-4172 (Electronic)
0092-8674 (Linking)},
   DOI = {10.1016/j.cell.2016.01.013},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/26824647},
   year = {2016},
   type = {Journal Article}
}

@article{RN4154,
   author = {Shen, W. and Gaskins, H. R. and McIntosh, M. K.},
   title = {Influence of dietary fat on intestinal microbes, inflammation, barrier function and metabolic outcomes},
   journal = {J Nutr Biochem},
   volume = {25},
   number = {3},
   pages = {270-80},
   ISSN = {1873-4847 (Electronic)
0955-2863 (Linking)},
   DOI = {10.1016/j.jnutbio.2013.09.009},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/24355793},
   year = {2014},
   type = {Journal Article}
}

@article{RN4068,
   author = {Smirnov, I. P.},
   title = {[Case of multiple race congenital abnormalities]},
   journal = {Vrach Delo},
   volume = {5},
   number = {5},
   pages = {130-1},
   ISSN = {0049-6804 (Print)
0049-6804 (Linking)},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/676255},
   year = {1978},
   type = {Journal Article}
}

@article{RN4082,
   author = {Song, S. J. and Lauber, C. and Costello, E. K. and Lozupone, C. A. and Humphrey, G. and Berg-Lyons, D. and Caporaso, J. G. and Knights, D. and Clemente, J. C. and Nakielny, S. and Gordon, J. I. and Fierer, N. and Knight, R.},
   title = {Cohabiting family members share microbiota with one another and with their dogs},
   journal = {Elife},
   volume = {2},
   pages = {e00458},
   ISSN = {2050-084X (Linking)},
   DOI = {10.7554/eLife.00458},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/23599893},
   year = {2013},
   type = {Journal Article}
}

@article{RN4136,
   author = {Sousa, T. and Paterson, R. and Moore, V. and Carlsson, A. and Abrahamsson, B. and Basit, A. W.},
   title = {The gastrointestinal microbiota as a site for the biotransformation of drugs},
   journal = {Int J Pharm},
   volume = {363},
   number = {1-2},
   pages = {1-25},
   ISSN = {0378-5173 (Print)
0378-5173 (Linking)},
   DOI = {10.1016/j.ijpharm.2008.07.009},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/18682282},
   year = {2008},
   type = {Journal Article}
}

@article{RN4084,
   author = {Spanogiannopoulos, P. and Bess, E. N. and Carmody, R. N. and Turnbaugh, P. J.},
   title = {The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism},
   journal = {Nat Rev Microbiol},
   volume = {14},
   number = {5},
   pages = {273-87},
   ISSN = {1740-1534 (Electronic)
1740-1526 (Linking)},
   DOI = {10.1038/nrmicro.2016.17},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/26972811},
   year = {2016},
   type = {Journal Article}
}

@article{RN4091,
   author = {Suzuki, T. and Masui, A. and Nakamura, J. and Shiozawa, H. and Aoki, J. and Nakae, H. and Tsuda, S. and Imai, J. and Hideki, O. and Matsushima, M. and Mine, T. and Tamura, A. and Ohtsu, T. and Asami, Y. and Takagi, A.},
   title = {Yogurt Containing Lactobacillus gasseri Mitigates Aspirin-Induced Small Bowel Injuries: A Prospective, Randomized, Double-Blind, Placebo-Controlled Trial},
   journal = {Digestion},
   volume = {95},
   number = {1},
   pages = {49-54},
   ISSN = {1421-9867 (Electronic)
0012-2823 (Linking)},
   DOI = {10.1159/000452361},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28052291},
   year = {2017},
   type = {Journal Article}
}

@article{RN4040,
   author = {Turnbaugh, P. J. and Ley, R. E. and Hamady, M. and Fraser-Liggett, C. M. and Knight, R. and Gordon, J. I.},
   title = {The human microbiome project},
   journal = {Nature},
   volume = {449},
   number = {7164},
   pages = {804-10},
   ISSN = {1476-4687 (Electronic)
0028-0836 (Linking)},
   DOI = {10.1038/nature06244},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/17943116},
   year = {2007},
   type = {Journal Article}
}

@article{RN4044,
   author = {Turnbaugh, P. J. and Ridaura, V. K. and Faith, J. J. and Rey, F. E. and Knight, R. and Gordon, J. I.},
   title = {The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice},
   journal = {Sci Transl Med},
   volume = {1},
   number = {6},
   pages = {6ra14},
   ISSN = {1946-6242 (Electronic)
1946-6234 (Linking)},
   DOI = {10.1126/scitranslmed.3000322},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/20368178},
   year = {2009},
   type = {Journal Article}
}

@article{RN4112,
   author = {Turroni, S. and Fiori, J. and Rampelli, S. and Schnorr, S. L. and Consolandi, C. and Barone, M. and Biagi, E. and Fanelli, F. and Mezzullo, M. and Crittenden, A. N. and Henry, A. G. and Brigidi, P. and Candela, M.},
   title = {Fecal metabolome of the Hadza hunter-gatherers: a host-microbiome integrative view},
   journal = {Sci Rep},
   volume = {6},
   pages = {32826},
   ISSN = {2045-2322 (Electronic)
2045-2322 (Linking)},
   DOI = {10.1038/srep32826},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27624970},
   year = {2016},
   type = {Journal Article}
}

@article{RN4137,
   author = {Van den Abbeele, P. and Grootaert, C. and Marzorati, M. and Possemiers, S. and Verstraete, W. and Gerard, P. and Rabot, S. and Bruneau, A. and El Aidy, S. and Derrien, M. and Zoetendal, E. and Kleerebezem, M. and Smidt, H. and Van de Wiele, T.},
   title = {Microbial community development in a dynamic gut model is reproducible, colon region specific, and selective for Bacteroidetes and Clostridium cluster IX},
   journal = {Appl Environ Microbiol},
   volume = {76},
   number = {15},
   pages = {5237-46},
   ISSN = {1098-5336 (Electronic)
0099-2240 (Linking)},
   DOI = {10.1128/AEM.00759-10},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/20562281},
   year = {2010},
   type = {Journal Article}
}

@inproceedings{Tem10,
  author = {Olivier Temam},
  booktitle = {International Symposium on Computer Architecture (ISCA)},
  title = {The Rebirth of Neural Networks},
  month = {June},
  year = {2010}
}

@article{RN4268,
   author = {Werner, J. J. and Knights, D. and Garcia, M. L. and Scalfone, N. B. and Smith, S. and Yarasheski, K. and Cummings, T. A. and Beers, A. R. and Knight, R. and Angenent, L. T.},
   title = {Bacterial community structures are unique and resilient in full-scale bioenergy systems},
   journal = {Proc Natl Acad Sci U S A},
   volume = {108},
   number = {10},
   pages = {4158-63},
   ISSN = {1091-6490 (Electronic)
0027-8424 (Linking)},
   DOI = {10.1073/pnas.1015676108},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/21368115},
   year = {2011},
   type = {Journal Article}
}

@article{RN4269,
   author = {Metcalf, J. L. and Xu, Z. Z. and Weiss, S. and Lax, S. and Van Treuren, W. and Hyde, E. R. and Song, S. J. and Amir, A. and Larsen, P. and Sangwan, N. and Haarmann, D. and Humphrey, G. C. and Ackermann, G. and Thompson, L. R. and Lauber, C. and Bibat, A. and Nicholas, C. and Gebert, M. J. and Petrosino, J. F. and Reed, S. C. and Gilbert, J. A. and Lynne, A. M. and Bucheli, S. R. and Carter, D. O. and Knight, R.},
   title = {Microbial community assembly and metabolic function during mammalian corpse decomposition},
   journal = {Science},
   volume = {351},
   number = {6269},
   pages = {158-62},
   ISSN = {1095-9203 (Electronic)
0036-8075 (Linking)},
   DOI = {10.1126/science.aad2646},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/26657285},
   year = {2016},
   type = {Journal Article}
}

@article{RN4270,
   author = {Chase, J. and Fouquier, J. and Zare, M. and Sonderegger, D. L. and Knight, R. and Kelley, S. T. and Siegel, J. and Caporaso, J. G.},
   title = {Geography and Location Are the Primary Drivers of Office Microbiome Composition},
   journal = {mSystems},
   volume = {1},
   number = {2},
   ISSN = {2379-5077 (Print)
2379-5077 (Linking)},
   DOI = {10.1128/mSystems.00022-16},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27822521},
   year = {2016},
   type = {Journal Article}
}

@article{RN4267,
   author = {Gilbert, J. A. and Jansson, J. K. and Knight, R.},
   title = {The Earth Microbiome project: successes and aspirations},
   journal = {BMC Biol},
   volume = {12},
   pages = {69},
   ISSN = {1741-7007 (Electronic)
1741-7007 (Linking)},
   DOI = {10.1186/s12915-014-0069-1},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/25184604},
   year = {2014},
   type = {Journal Article}
}

@article{RN4266,
   author = {Ibsen-Jensen, R. and Chatterjee, K. and Nowak, M. A.},
   title = {Computational complexity of ecological and evolutionary spatial dynamics},
   journal = {Proc Natl Acad Sci U S A},
   volume = {112},
   number = {51},
   pages = {15636-41},
   ISSN = {1091-6490 (Electronic)
0027-8424 (Linking)},
   DOI = {10.1073/pnas.1511366112},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/26644569},
   year = {2015},
   type = {Journal Article}
}

@article{RN4129,
   author = {van Nood, E. and Vrieze, A. and Nieuwdorp, M. and Fuentes, S. and Zoetendal, E. G. and de Vos, W. M. and Visser, C. E. and Kuijper, E. J. and Bartelsman, J. F. and Tijssen, J. G. and Speelman, P. and Dijkgraaf, M. G. and Keller, J. J.},
   title = {Duodenal infusion of donor feces for recurrent Clostridium difficile},
   journal = {N Engl J Med},
   volume = {368},
   number = {5},
   pages = {407-15},
   ISSN = {1533-4406 (Electronic)
0028-4793 (Linking)},
   DOI = {10.1056/NEJMoa1205037},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/23323867},
   year = {2013},
   type = {Journal Article}
}

@article{RN4063,
   author = {Vazquez-Baeza, Y. and Gonzalez, A. and Smarr, L. and McDonald, D. and Morton, J. T. and Navas-Molina, J. A. and Knight, R.},
   title = {Bringing the Dynamic Microbiome to Life with Animations},
   journal = {Cell Host Microbe},
   volume = {21},
   number = {1},
   pages = {7-10},
   ISSN = {1934-6069 (Electronic)
1931-3128 (Linking)},
   DOI = {10.1016/j.chom.2016.12.009},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28081445},
   year = {2017},
   type = {Journal Article}
}

@article{RN4179,
   author = {Vazquez-Baeza, Y. and Hyde, E. R. and Suchodolski, J. S. and Knight, R.},
   title = {Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks},
   journal = {Nat Microbiol},
   volume = {1},
   pages = {16177},
   ISSN = {2058-5276 (Electronic)
2058-5276 (Linking)},
   DOI = {10.1038/nmicrobiol.2016.177},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27694806},
   year = {2016},
   type = {Journal Article}
}

@article{RN4192,
   author = {Vega-Lopez, S. and Ausman, L. M. and Griffith, J. L. and Lichtenstein, A. H.},
   title = {Interindividual variability and intra-individual reproducibility of glycemic index values for commercial white bread},
   journal = {Diabetes Care},
   volume = {30},
   number = {6},
   pages = {1412-7},
   ISSN = {1935-5548 (Electronic)
0149-5992 (Linking)},
   DOI = {10.2337/dc06-1598},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/17384339},
   year = {2007},
   type = {Journal Article}
}

@article{RN4191,
   author = {Vrolix, R. and Mensink, R. P.},
   title = {Variability of the glycemic response to single food products in healthy subjects},
   journal = {Contemp Clin Trials},
   volume = {31},
   number = {1},
   pages = {5-11},
   ISSN = {1559-2030 (Electronic)
1551-7144 (Linking)},
   DOI = {10.1016/j.cct.2009.08.001},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/19737630},
   year = {2010},
   type = {Journal Article}
}

@article{RN4182,
   author = {Wang, M. and Carver, J. J. and Phelan, V. V. and Sanchez, L. M. and Garg, N. and Peng, Y. and Nguyen, D. D. and Watrous, J. and Kapono, C. A. and Luzzatto-Knaan, T. and Porto, C. and Bouslimani, A. and Melnik, A. V. and Meehan, M. J. and Liu, W. T. and Crusemann, M. and Boudreau, P. D. and Esquenazi, E. and Sandoval-Calderon, M. and Kersten, R. D. and Pace, L. A. and Quinn, R. A. and Duncan, K. R. and Hsu, C. C. and Floros, D. J. and Gavilan, R. G. and Kleigrewe, K. and Northen, T. and Dutton, R. J. and Parrot, D. and Carlson, E. E. and Aigle, B. and Michelsen, C. F. and Jelsbak, L. and Sohlenkamp, C. and Pevzner, P. and Edlund, A. and McLean, J. and Piel, J. and Murphy, B. T. and Gerwick, L. and Liaw, C. C. and Yang, Y. L. and Humpf, H. U. and Maansson, M. and Keyzers, R. A. and Sims, A. C. and Johnson, A. R. and Sidebottom, A. M. and Sedio, B. E. and Klitgaard, A. and Larson, C. B. and Boya, P. Ca and Torres-Mendoza, D. and Gonzalez, D. J. and Silva, D. B. and Marques, L. M. and Demarque, D. P. and Pociute, E. and O'Neill, E. C. and Briand, E. and Helfrich, E. J. and Granatosky, E. A. and Glukhov, E. and Ryffel, F. and Houson, H. and Mohimani, H. and Kharbush, J. J. and Zeng, Y. and Vorholt, J. A. and Kurita, K. L. and Charusanti, P. and McPhail, K. L. and Nielsen, K. F. and Vuong, L. and Elfeki, M. and Traxler, M. F. and Engene, N. and Koyama, N. and Vining, O. B. and Baric, R. and Silva, R. R. and Mascuch, S. J. and Tomasi, S. and Jenkins, S. and Macherla, V. and Hoffman, T. and Agarwal, V. and Williams, P. G. and Dai, J. and Neupane, R. and Gurr, J. and Rodriguez, A. M. and Lamsa, A. and Zhang, C. and Dorrestein, K. and Duggan, B. M. and Almaliti, J. and Allard, P. M. and Phapale, P. and others },
   title = {Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking},
   journal = {Nat Biotechnol},
   volume = {34},
   number = {8},
   pages = {828-37},
   ISSN = {1546-1696 (Electronic)
1087-0156 (Linking)},
   DOI = {10.1038/nbt.3597},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27504778},
   year = {2016},
   type = {Journal Article}
}

@article{RN4155,
   author = {Watanabe, M. and Houten, S. M. and Mataki, C. and Christoffolete, M. A. and Kim, B. W. and Sato, H. and Messaddeq, N. and Harney, J. W. and Ezaki, O. and Kodama, T. and Schoonjans, K. and Bianco, A. C. and Auwerx, J.},
   title = {Bile acids induce energy expenditure by promoting intracellular thyroid hormone activation},
   journal = {Nature},
   volume = {439},
   number = {7075},
   pages = {484-9},
   ISSN = {1476-4687 (Electronic)
0028-0836 (Linking)},
   DOI = {10.1038/nature04330},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/16400329},
   year = {2006},
   type = {Journal Article}
}

@article{RN4183,
   author = {Watrous, J. and Roach, P. and Alexandrov, T. and Heath, B. S. and Yang, J. Y. and Kersten, R. D. and van der Voort, M. and Pogliano, K. and Gross, H. and Raaijmakers, J. M. and Moore, B. S. and Laskin, J. and Bandeira, N. and Dorrestein, P. C.},
   title = {Mass spectral molecular networking of living microbial colonies},
   journal = {Proc Natl Acad Sci U S A},
   volume = {109},
   number = {26},
   pages = {E1743-52},
   ISSN = {1091-6490 (Electronic)
0027-8424 (Linking)},
   DOI = {10.1073/pnas.1203689109},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/22586093},
   year = {2012},
   type = {Journal Article}
}

@article{RN4185,
   author = {Weiss, S. and Van Treuren, W. and Lozupone, C. and Faust, K. and Friedman, J. and Deng, Y. and Xia, L. C. and Xu, Z. Z. and Ursell, L. and Alm, E. J. and Birmingham, A. and Cram, J. A. and Fuhrman, J. A. and Raes, J. and Sun, F. and Zhou, J. and Knight, R.},
   title = {Correlation detection strategies in microbial data sets vary widely in sensitivity and precision},
   journal = {ISME J},
   volume = {10},
   number = {7},
   pages = {1669-81},
   ISSN = {1751-7370 (Electronic)
1751-7362 (Linking)},
   DOI = {10.1038/ismej.2015.235},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/26905627},
   year = {2016},
   type = {Journal Article}
}

@article{RN4173,
   author = {Willing, B. P. and Dicksved, J. and Halfvarson, J. and Andersson, A. F. and Lucio, M. and Zheng, Z. and Jarnerot, G. and Tysk, C. and Jansson, J. K. and Engstrand, L.},
   title = {A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes},
   journal = {Gastroenterology},
   volume = {139},
   number = {6},
   pages = {1844-1854 e1},
   ISSN = {1528-0012 (Electronic)
0016-5085 (Linking)},
   DOI = {10.1053/j.gastro.2010.08.049},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/20816835},
   year = {2010},
   type = {Journal Article}
}

@article{RN4088,
   author = {Wu, G. D. and Chen, J. and Hoffmann, C. and Bittinger, K. and Chen, Y. Y. and Keilbaugh, S. A. and Bewtra, M. and Knights, D. and Walters, W. A. and Knight, R. and Sinha, R. and Gilroy, E. and Gupta, K. and Baldassano, R. and Nessel, L. and Li, H. and Bushman, F. D. and Lewis, J. D.},
   title = {Linking long-term dietary patterns with gut microbial enterotypes},
   journal = {Science},
   volume = {334},
   number = {6052},
   pages = {105-8},
   ISSN = {1095-9203 (Electronic)
0036-8075 (Linking)},
   DOI = {10.1126/science.1208344},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/21885731},
   year = {2011},
   type = {Journal Article}
}

@article{RN4127,
   author = {Wu, H. and Esteve, E. and Tremaroli, V. and Khan, M. T. and Caesar, R. and Manneras-Holm, L. and Stahlman, M. and Olsson, L. M. and Serino, M. and Planas-Felix, M. and Xifra, G. and Mercader, J. M. and Torrents, D. and Burcelin, R. and Ricart, W. and Perkins, R. and Fernandez-Real, J. M. and Backhed, F.},
   title = {Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug},
   journal = {Nat Med},
   ISSN = {1546-170X (Electronic)
1078-8956 (Linking)},
   DOI = {10.1038/nm.4345},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28530702},
   year = {2017},
   type = {Journal Article}
}

@article{RN4089,
   author = {Xiao, X. and Nakatsu, G. and Jin, Y. and Wong, S. and Yu, J. and Lau, J. Y.},
   title = {Gut Microbiota Mediates Protection Against Enteropathy Induced by Indomethacin},
   journal = {Sci Rep},
   volume = {7},
   pages = {40317},
   ISSN = {2045-2322 (Electronic)
2045-2322 (Linking)},
   DOI = {10.1038/srep40317},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28067296},
   year = {2017},
   type = {Journal Article}
}

@article{RN4061,
   author = {Yatsunenko, T. and Rey, F. E. and Manary, M. J. and Trehan, I. and Dominguez-Bello, M. G. and Contreras, M. and Magris, M. and Hidalgo, G. and Baldassano, R. N. and Anokhin, A. P. and Heath, A. C. and Warner, B. and Reeder, J. and Kuczynski, J. and Caporaso, J. G. and Lozupone, C. A. and Lauber, C. and Clemente, J. C. and Knights, D. and Knight, R. and Gordon, J. I.},
   title = {Human gut microbiome viewed across age and geography},
   journal = {Nature},
   volume = {486},
   number = {7402},
   pages = {222-7},
   ISSN = {1476-4687 (Electronic)
0028-0836 (Linking)},
   DOI = {10.1038/nature11053},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/22699611},
   year = {2012},
   type = {Journal Article}
}

@article{RN4124,
   author = {Yoshikawa, K. and Kurihara, C. and Furuhashi, H. and Takajo, T. and Maruta, K. and Yasutake, Y. and Sato, H. and Narimatsu, K. and Okada, Y. and Higashiyama, M. and Watanabe, C. and Komoto, S. and Tomita, K. and Nagao, S. and Miura, S. and Tajiri, H. and Hokari, R.},
   title = {Psychological stress exacerbates NSAID-induced small bowel injury by inducing changes in intestinal microbiota and permeability via glucocorticoid receptor signaling},
   journal = {J Gastroenterol},
   volume = {52},
   number = {1},
   pages = {61-71},
   ISSN = {1435-5922 (Electronic)
0944-1174 (Linking)},
   DOI = {10.1007/s00535-016-1205-1},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27075753},
   year = {2017},
   type = {Journal Article}
}

@article{RN4142,
   author = {Zanger, U. M. and Schwab, M.},
   title = {Cytochrome P450 enzymes in drug metabolism: regulation of gene expression, enzyme activities, and impact of genetic variation},
   journal = {Pharmacol Ther},
   volume = {138},
   number = {1},
   pages = {103-41},
   ISSN = {1879-016X (Electronic)
0163-7258 (Linking)},
   DOI = {10.1016/j.pharmthera.2012.12.007},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/23333322},
   year = {2013},
   type = {Journal Article}
}

@article{RN4181,
   author = {Zeevi, D. and Korem, T. and Zmora, N. and Israeli, D. and Rothschild, D. and Weinberger, A. and Ben-Yacov, O. and Lador, D. and Avnit-Sagi, T. and Lotan-Pompan, M. and Suez, J. and Mahdi, J. A. and Matot, E. and Malka, G. and Kosower, N. and Rein, M. and Zilberman-Schapira, G. and Dohnalova, L. and Pevsner-Fischer, M. and Bikovsky, R. and Halpern, Z. and Elinav, E. and Segal, E.},
   title = {Personalized Nutrition by Prediction of Glycemic Responses},
   journal = {Cell},
   volume = {163},
   number = {5},
   pages = {1079-94},
   ISSN = {1097-4172 (Electronic)
0092-8674 (Linking)},
   DOI = {10.1016/j.cell.2015.11.001},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/26590418},
   year = {2015},
   type = {Journal Article}
}

@article{RN4070,
   author = {Zhang, Z. and Geng, J. and Tang, X. and Fan, H. and Xu, J. and Wen, X. and Ma, Z. S. and Shi, P.},
   title = {Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota},
   journal = {ISME J},
   volume = {8},
   number = {4},
   pages = {881-93},
   ISSN = {1751-7370 (Electronic)
1751-7362 (Linking)},
   DOI = {10.1038/ismej.2013.185},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/24132077},
   year = {2014},
   type = {Journal Article}
}

@article{RN4059,
   author = {Zhernakova, A. and Kurilshikov, A. and Bonder, M. J. and Tigchelaar, E. F. and Schirmer, M. and Vatanen, T. and Mujagic, Z. and Vila, A. V. and Falony, G. and Vieira-Silva, S. and Wang, J. and Imhann, F. and Brandsma, E. and Jankipersadsing, S. A. and Joossens, M. and Cenit, M. C. and Deelen, P. and Swertz, M. A. and LifeLines cohort, study and Weersma, R. K. and Feskens, E. J. and Netea, M. G. and Gevers, D. and Jonkers, D. and Franke, L. and Aulchenko, Y. S. and Huttenhower, C. and Raes, J. and Hofker, M. H. and Xavier, R. J. and Wijmenga, C. and Fu, J.},
   title = {Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity},
   journal = {Science},
   volume = {352},
   number = {6285},
   pages = {565-9},
   ISSN = {1095-9203 (Electronic)
0036-8075 (Linking)},
   DOI = {10.1126/science.aad3369},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27126040},
   year = {2016},
   type = {Journal Article}
}

@article{RN4067,
   author = {Zoetendal, E. G. and Raes, J. and van den Bogert, B. and Arumugam, M. and Booijink, C. C. and Troost, F. J. and Bork, P. and Wels, M. and de Vos, W. M. and Kleerebezem, M.},
   title = {The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates},
   journal = {ISME J},
   volume = {6},
   number = {7},
   pages = {1415-26},
   ISSN = {1751-7370 (Electronic)
1751-7362 (Linking)},
   DOI = {10.1038/ismej.2011.212},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/22258098},
   year = {2012},
   type = {Journal Article}
}


@article{RN4205,
   author = {Breiman, L.},
   title = {Random Forests},
   journal = {Machine Learning},
   volume = {45},
   number = {1},
   pages = {5-32},
   year = {2001},
   type = {Journal Article}
}

@unpublished{RN4216,
   author = {Christ, M. and Kempa-Liehr and A.W. and Feindt, M},
   title = {Distributed and parallel time series feature extraction for industrial big data applications.},
   address = {https://arxiv.org/},
   DOI = {arXiv:1610.07717v3},
   url = {https://arxiv.org/abs/1610.07717},
   year = {2017},
   type = {Unpublished Work}
}

@article{RN4007,
   author = {Faith, D. P. and Baker, A. M.},
   title = {Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges},
   journal = {Evol Bioinform Online},
   volume = {2},
   pages = {121-8},
   ISSN = {1176-9343 (Electronic)
1176-9343 (Linking)},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19455206},
   year = {2006},
   type = {Journal Article}
}

@article{RN4263,
   author = {Knights, D. and Silverberg, M. S. and Weersma, R. K. and Gevers, D. and Dijkstra, G. and Huang, H. and Tyler, A. D. and van Sommeren, S. and Imhann, F. and Stempak, J. M. and Huang, H. and Vangay, P. and Al-Ghalith, G. A. and Russell, C. and Sauk, J. and Knight, J. and Daly, M. J. and Huttenhower, C. and Xavier, R. J.},
   title = {Complex host genetics influence the microbiome in inflammatory bowel disease},
   journal = {Genome Med},
   volume = {6},
   number = {12},
   pages = {107},
   ISSN = {1756-994X (Print)
1756-994X (Linking)},
   DOI = {10.1186/s13073-014-0107-1},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/25587358},
   year = {2014},
   type = {Journal Article}
}

@article{RN4264,
   author = {Jacobs, J. P. and Goudarzi, M. and Singh, N. and Tong, M. and McHardy, I. H. and Ruegger, P. and Asadourian, M. and Moon, B. H. and Ayson, A. and Borneman, J. and McGovern, D. P. and Fornace, A. J., Jr. and Braun, J. and Dubinsky, M.},
   title = {A Disease-Associated Microbial and Metabolomics State in Relatives of Pediatric Inflammatory Bowel Disease Patients},
   journal = {Cell Mol Gastroenterol Hepatol},
   volume = {2},
   number = {6},
   pages = {750-766},
   ISSN = {2352-345X (Print)
2352-345X (Linking)},
   DOI = {10.1016/j.jcmgh.2016.06.004},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28174747},
   year = {2016},
   type = {Journal Article}
}


@article{RN4217,
   author = {Frank, D. N. and St Amand, A. L. and Feldman, R. A. and Boedeker, E. C. and Harpaz, N. and Pace, N. R.},
   title = {Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases},
   journal = {Proc Natl Acad Sci U S A},
   volume = {104},
   number = {34},
   pages = {13780-5},
   ISSN = {0027-8424 (Print)
0027-8424 (Linking)},
   DOI = {10.1073/pnas.0706625104},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/17699621},
   year = {2007},
   type = {Journal Article}
}

@article{RN4208,
   author = {Pascal, V. and Pozuelo, M. and Borruel, N. and Casellas, F. and Campos, D. and Santiago, A. and Martinez, X. and Varela, E. and Sarrabayrouse, G. and Machiels, K. and Vermeire, S. and Sokol, H. and Guarner, F. and Manichanh, C.},
   title = {A microbial signature for Crohn's disease},
   journal = {Gut},
   volume = {66},
   number = {5},
   pages = {813-822},
   ISSN = {1468-3288 (Electronic)
0017-5749 (Linking)},
   DOI = {10.1136/gutjnl-2016-313235},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28179361},
   year = {2017},
   type = {Journal Article}
}

@article{RN4219,
   author = {Sartor, R. B. and Wu, G. D.},
   title = {Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches},
   journal = {Gastroenterology},
   volume = {152},
   number = {2},
   pages = {327-339 e4},
   ISSN = {1528-0012 (Electronic)
0016-5085 (Linking)},
   DOI = {10.1053/j.gastro.2016.10.012},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27769810},
   year = {2017},
   type = {Journal Article}
}

@article{RN4204,
   author = {Washburne, A. D. and Silverman, J. D. and Leff, J. W. and Bennett, D. J. and Darcy, J. L. and Mukherjee, S. and Fierer, N. and David, L. A.},
   title = {Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets},
   journal = {PeerJ},
   volume = {5},
   pages = {e2969},
   DOI = {10.7717/peerj.2969},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28289558},
   year = {2017},
   type = {Journal Article}
}

@article{Caporaso2011proceedings, title={Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample}, volume={108}, ISSN={0027-8424}, DOI={10.1073/pnas.1000080107},  note={01135}, number={Suppl 1}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Caporaso, J. Gregory and Lauber, Christian L. and Walters, William A. and Berg-Lyons, Donna and Lozupone, Catherine A. and Turnbaugh, Peter J. and Fierer, Noah and Knight, Rob}, year={2011}, month={Mar}, pages={4516-4522}}

@article{Ihaka1996, title={R: A Language for Data Analysis and Graphics}, volume={5}, ISSN={10618600}, DOI={10.2307/1390807}, note={08748}, number={3}, journal={Journal of Computational and Graphical Statistics}, author={Ihaka, Ross and Gentleman, Robert}, year={1996}, month={Sep}, pages={299}}

@article{Jostins2012, title={Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease}, volume={491}, ISSN={0028-0836}, DOI={10.1038/nature11582},  note={01571}, number={7422}, journal={Nature}, author={Jostins, L. and Ripke, S. and Weersma, R. K. and Duerr, R. H. and McGovern, D. P. and Hui, K. Y. and Lee, J. C. and Schumm, L. P. and Sharma, Y. and Anderson, C. A. and Essers, J. and Mitrovic, M. and Ning, K. and Cleynen, I. and Theatre, E. and Spain, S. L. and Raychaudhuri, S. and Goyette, P. and Wei, Z. and Abraham, C. and Achkar, J. P. and Ahmad, T. and Amininejad, L. and Ananthakrishnan, A. N. and Andersen, V. and Andrews, J.  M. and Baidoo, L. and Balschun, T. and Bampton, P. A. and Bitton, A. and Boucher, G. and Brand, S. and Buning, C. and Cohain, A. and Cichon, S. and D'Amato, M. and De Jong, D. and Devaney, K. L. and Dubinsky, M. and Edwards, C. and Ellinghaus, D. and Ferguson, L. R. and Franchimont, D. and Fransen, K. and Gearry, R. and Georges, M. and Gieger, C. and Glas, J. and Haritunians, T. and Hart, A. and Hawkey, C. and Hedl, M. and Hu, X. and Karlsen, T. H. and Kupcinskas, L. and Kugathasan, S. and Latiano, A. and Laukens, D. and Lawrance, I. C. and Lees, C. W. and Louis, E. and Mahy, G.  and Mansfield, J. and Morgan, A. R. and Mowat, C. and Newman, W. and Palmieri, O. and Ponsioen, C. Y. and Potocnik, U. and Prescott, N. J. and Regueiro, M. and Rotter, J. I. and Russell, R. K. and Sanderson, J. D. and Sans, M. and Satsangi, J. and Schreiber, S. and Simms, L. A. and Sventoraityte, J. and Targan, S. R. and Taylor, K. D. and Tremelling, M.  and Verspaget, H. W. and De Vos, M. and Wijmenga, C. and Wilson, D. C. and Winkelmann, J. and Xavier, R. J. and Zeissig, S. and Zhang, B. and Zhang, C. K. and Zhao, H. and International, I. B. D. Genetics Consortium and Silverberg, M. S. and Annese, V. and Hakonarson, H. and Brant, S. R. and Radford-Smith, G. and Mathew, C. G. and Rioux, J. D. and Schadt, EE and Daly, MJ and Franke, A and Parkes, M and Vermeire, S and Barrett, JC and Cho, JH }, year={2012}, month={Nov}, pages={119-124}}

@article{Knights2011, title={Human-associated microbial signatures: examining their predictive value}, volume={10}, ISSN={1931-3128}, url={http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3879110/}, DOI={10.1016/j.chom.2011.09.003}, note={00048}, number={4}, journal={Cell host \& microbe}, author={Knights, Dan and Parfrey, Laura Wegener and Zaneveld, Jesse and Lozupone, Catherine and Knight, Rob}, year={2011}, month={Oct}}

@article{Kolho2015, title={Fecal Microbiota in Pediatric Inflammatory Bowel Disease and Its Relation to Inflammation}, volume={110}, ISSN={0002-9270}, DOI={10.1038/ajg.2015.149},  note={00024}, number={6}, journal={The American Journal of Gastroenterology}, author={Kolho, Kaija-Leena and Korpela, Katri and Jaakkola, Tytti and Pichai, Madharasi V. A. and Zoetendal, Erwin G. and Salonen, Anne and de Vos, Willem M.}, year={2015}, month={Jun}, pages={921-930}} 
@article{Lewis2011, title={The Utility of Biomarkers in the Diagnosis and Therapy of Inflammatory Bowel Disease}, volume={140}, ISSN={0016-5085}, DOI={10.1053/j.gastro.2010.11.058},  note={00000}, number={6}, journal={Gastroenterology}, author={Lewis, James D.}, year={2011}, month={May}, pages={1817-1826.e2}}

@article{Liaw2002, title={Classification and Regression by randomForest}, volume={2}, note={03910}, number={3}, journal={R News}, author={Liaw, Andy and Wiener, Matthew}, year={2002}, pages={18-22}}

@article{Locke2015, title={Genetic studies of body mass index yield new insights for obesity biology}, volume={518}, ISSN={0028-0836}, DOI={10.1038/nature14177},  note={00449}, number={7538}, journal={Nature}, author={Locke, A. E. and Kahali, B. and Berndt, S. I. and Justice, A. E. and Pers, T. H. and Day, F. R. and Powell, C. and Vedantam, S. and Buchkovich, M. L. and Yang, J. and Croteau-Chonka, D. C. and Esko, T. and Fall, T. and Ferreira, T. and Gustafsson, S. and Kutalik, Z. and Luan, J. and Magi, R. and Randall, J. C. and Winkler, T. W. and Wood, A. R. and Workalemahu, T. and Faul, J. D. and Smith, J. A. and Zhao, J. H. and Zhao, W. and Chen, J. and Fehrmann, R. and Hedman, A. K. and Karjalainen, J. and Schmidt, E. M. and Absher, D. and Amin, N. and Anderson, D. and Beekman, M. and Bolton, J. L. and Bragg-Gresham, J. L. and Buyske, S. and Demirkan, A. and Deng, G. and Ehret, G. B. and Feenstra, B. and Feitosa, M. F. and Fischer, K. and Goel, A. and Gong, J. and Jackson, A. U. and Kanoni, S. and Kleber, M. E. and Kristiansson, K. and Lim, U. and Lotay, V. and Mangino, M. and Leach, I. M. and Medina-Gomez, C. and Medland, S. E. and Nalls, M. A. and Palmer, C. D. and Pasko, D. and Pechlivanis, S. and Peters, M. J. and Prokopenko, I. and Shungin, D. and Stancakova, A. and Strawbridge, R. J. and Sung, Y. J. and Tanaka, T. and Teumer, A. and Trompet, S. and van der Laan, S. W. and van Setten, J. and Van Vliet-Ostaptchouk, J. V. and Wang, Z. and Yengo, L. and Zhang, W. and Isaacs, A. and Albrecht, E. and Arnlov, J. and Arscott, G. M. and Attwood, A. P. and Bandinelli, S. and Barrett, A. and Bas, I. N. and Bellis, C. and Bennett, A. J. and Berne, C. and Blagieva, R. and Bluher, M. and Bohringer, S. and Bonnycastle, L. L. and Bottcher, Y. and Boyd, H. A. and Bruinenberg, M. and Caspersen, I. H. and Chen, Y. I. and Clarke, R. and Daw, E. W. and de Craen, A. J. M. and Delgado, G. and Dimitriou, M.}, year={2015}, month={Feb}, pages={197-206}}

@article{Love2014, title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2}, volume={15}, ISSN={1465-6906}, url={http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302049/}, DOI={10.1186/s13059-014-0550-8}, note={01282}, number={12}, journal={Genome Biology}, author={Love, Michael I and Huber, Wolfgang and Anders, Simon}, year={2014}}

@article{Manichanh2012, title={The gut microbiota in IBD}, volume={9}, ISSN={1759-5045}, DOI={10.1038/nrgastro.2012.152}, note={00418}, number={10}, journal={Nature Reviews Gastroenterology and Hepatology}, author={Manichanh, Chaysavanh and Borruel, Natalia and Casellas, Francesc and Guarner, Francisco}, year={2012}, month={Oct}, pages={599-608}}

@article{Martinez2008, title={Unstable Composition of the Fecal Microbiota in Ulcerative Colitis During Clinical Remission}, volume={103}, ISSN={0002-9270}, DOI={10.1111/j.1572-0241.2007.01592.x}, note={00114}, number={3}, journal={The American Journal of Gastroenterology}, author={Martinez, Cristina and Antolin, Maria and Santos, Javier and Torrejon, Antonio and Casellas, Francesc and Borruel, Natalia and Guarner, Francisco and Malagelada, Juan-R.}, year={2008}, month={Mar}, pages={643-648}}

@article{Martinez2013, title={Gut microbiome composition is linked to whole grain-induced immunological improvements}, volume={7}, ISSN={1751-7362}, DOI={10.1038/ismej.2012.104},  note={00104}, number={2}, journal={The ISME Journal}, author={Martinez, Ines and Lattimer, James M. and Hubach, Kelcie L. and Case, Jennifer A. and Yang, Junyi and Weber, Casey G. and Louk, Julie A. and Rose, Devin J. and Kyureghian, Gayaneh and Peterson, Daniel A. and Haub M. and Walter J.}, year={2013}, month={Feb}, pages={269-280}}

@article{McMurdie2013, title={phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data}, volume={8}, DOI={10.1371/journal.pone.0061217},  note={00352}, number={4}, journal={PLoS ONE}, author={McMurdie, Paul J. and Holmes, Susan}, year={2013}, month={Apr}, pages={e61217}}

@book{Oksanen2016, title={vegan: Community Ecology Package}, url={https://cran.r-project.org/web/packages/vegan/index.html}, abstractNote={Ordination methods, diversity analysis and otherfunctions for community and vegetation ecologists.}, note={00000}, author={Oksanen, Jari and Blanchet, F. Guillaume and Friendly, Michael and Kindt, Roeland and Legendre, Pierre and McGlinn, Dan and Minchin, Peter R. and O'Hara, R. B. and Simpson, Gavin L. and Solymos, Peter and the Vegan Development Team}, year={2016}, month={Jun}}

@article{Rajca2014, title={Alterations in the intestinal microbiome (dysbiosis) as a predictor of relapse after infliximab withdrawal in Crohn's disease}, volume={20}, ISSN={1536-4844}, DOI={10.1097/MIB.0000000000000036}, note={00034}, number={6}, journal={Inflammatory Bowel Diseases}, author={Rajca, Sylvie and Grondin, Virginie and Louis, Edouard and Vernier-Massouille, Gwenola and Grimaud, Jean-Charle and Bouhnik, Yoram and Laharie, David and Dupas, Jean-Louis and Pillant, Helene and Picon, Laurence and Veyrac, M and Flamant, Mand  Savoye, G and Jian, R and Devos, M and Paintaud, G and Piver, E and Allez, M and Mary, JY and Sokol, H and Colombel, JF and Seksik, P}, year={2014}, month={Jun}, pages={978-986}}

@article{Rooks2014, title={Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission}, volume={8}, ISSN={1751-7362}, DOI={10.1038/ismej.2014.3},  note={00067}, number={7}, journal={The ISME Journal}, author={Rooks, Michelle G and Veiga, Patrick and Wardwell-Scott, Leslie H and Tickle, Timothy and Segata, Nicola and Michaud, Monia and Gallini, Carey Ann and Beal, Chlo\'{e} and van Hylckama-Vlieg, Johan ET and Ballal, Sonia A and Morgan, X and Glickman, J and Gevers, D and Huttenhower, C and Garret, W}, year={2014}, month={Jul}, pages={1403-1417}}

@article{Silverberg2005, title={Toward an integrated clinical, molecular and serological classification of inflammatory bowel disease: report of a Working Party of the 2005 Montreal World Congress of Gastroenterology}, volume={19 Suppl A}, ISSN={1916-7237},  note={00000}, journal={Canadian Journal of Gastroenterology = Journal Canadien De Gastroenterologie}, author={Silverberg, Mark S. and Satsangi, Jack and Ahmad, Tariq and Arnott, Ian D. R. and Bernstein, Charles N. and Brant, Steven R. and Caprilli, Renzo and Colombel, Jean-Fr\'{e}d\'{e}ric and Gasche, Christoph and Geboes, Karel and Jewel, D and Karban, A and Loftus, EV Jr andPena, A and Riddel, RH and Sachar, DB and Schreiber, S and Steinhart, AH and Targan, SR and Vermeire, S and Warren, BF}, year={2005}, month={Sep}, pages={5A-36A}}

@article{RN4265,
   author = {Satsangi, J. and Silverberg, M. S. and Vermeire, S. and Colombel, J. F.},
   title = {The Montreal classification of inflammatory bowel disease: controversies, consensus, and implications},
   journal = {Gut},
   volume = {55},
   number = {6},
   pages = {749-53},
   ISSN = {0017-5749 (Print)
0017-5749 (Linking)},
   DOI = {10.1136/gut.2005.082909},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/16698746},
   year = {2006},
   type = {Journal Article}
}

@article{FowlerWegel1922,
   author = {Fowler, E. P. and Wegel R. L.},
   title = {Presentation of a new instrument for determining the amount of character of auditory sensation},
   journal = {Trans Am Otol Soc},
   volume = {16},
   pages = {105-123},
   year = {1922},
   type = {Journal Article}
}
@article{ECGZywietz,
   author = {Zywietz, C.},
   title = {A brief history of electrocardiography - progress through technology},
   type = {Journal Article},
   journal = {Published Online by Biosigna, Institute for Biosignal Processing and System Analysis}
}

@book{WebsetrEncyclopeida,
 author = {Webster, John G.},
 title = {Encyclopedia of Medical Devices and Instrumentation},
 year = {1990},
 isbn = {0471829366},
 edition = {1st},
 publisher = {John Wiley \& Sons, Inc.},
 address = {New York, NY, USA},
}

@article{njem_ecg,
    author = { Willems ,  Jos L.  and  Abreu-Lima ,  Cassiano  and  Arnaud ,  Pierre  and  van Bemmel ,  Jan H.  and  Brohet ,  Christian  and  Degani ,  Rosanna  and  Denis ,  Bernard  and  Gehring ,  Jürgen  and  Graham ,  Ian  and  van Herpen ,  Gerard  and  Machado ,  Hilario  and  Macfarlane ,  Peter W.  and  Michaelis ,  Jörg  and  Moulopoulos ,  Spyridon D.  and  Rubel ,  Paul  and  Zywietz ,  Christoph },
    title = {The Diagnostic Performance of Computer Programs for the Interpretation of Electrocardiograms},
    journal = {New England Journal of Medicine},
    volume = {325},
    number = {25},
    pages = {1767-1773},
    year = {1991},
    doi = {10.1056/NEJM199112193252503},
    note ={PMID: 1834940},

    URL = { http://dx.doi.org/10.1056/NEJM199112193252503 },
    eprint = { http://dx.doi.org/10.1056/NEJM199112193252503 }
}

@article {Gibbons165910,
	author = {Gibbons, Sean and Duvallet, Claire and Alm, Eric J.},
	title = {Correcting for batch effects in case-control microbiome studies},
	year = {2017},
	doi = {10.1101/165910},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {High-throughput data generation platforms, like mass-spectrometry, microarrays, and second-generation sequencing are susceptible to batch effects due to run-to-run variation in reagents, equipment, protocols, or personnel. Currently, batch correction methods are not commonly applied to microbiome sequencing datasets. In this paper, we compare multiple batch-correction methods applied to microbiome case-control studies. We introduce a model-free normalization procedure where features (i.e. bacterial taxa) in case samples are converted to percentiles of the equivalent features in control samples within a study prior to pooling data across studies. We look at how this percentile-normalization method compares to ComBat, a widely used batch-correction model developed for RNA microarray data, and traditional meta-analysis methods for combining independent p-values. Overall, we show that percentile-normalization is a simple, model-free approach for removing batch effects and improving sensitivity in case-control meta-analyses.},
	URL = {https://www.biorxiv.org/content/early/2017/07/24/165910},
	eprint = {https://www.biorxiv.org/content/early/2017/07/24/165910.full.pdf},
	journal = {bioRxiv}
}

@article{Sipponen2008, title={Correlation of faecal calprotectin and lactoferrin with an endoscopic score for Crohn's disease and histological findings}, volume={28}, ISSN={1365-2036}, DOI={10.1111/j.1365-2036.2008.03835.x},  note={00000}, number={10}, journal={Alimentary Pharmacology \& Therapeutics}, author={Sipponen, T. and K\"{a}rkk\"{a}inen, P. and Savilahti, E. and Kolho, K.-L. and Nuutinen, H. and Turunen, U. and F\"{a}rkkil\"{a} M.}, year={2008}, month={Nov}, pages={1221-1229}}

@article{Sokol2008, title={Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients}, volume={105}, ISSN={0027-8424}, DOI={10.1073/pnas.0804812105}, note={01592}, number={43}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Sokol, Harry and Pigneur, B\'{e}n\'{e}dicte and Watterlot, Laurie and Lakhdari, Omar and Bermedez-Humaron, Luis G. and Gratadoux, Jean-Jacques and Blugeon, S\'{e}bastien and Bridonneau, Chantal and Furet, Jean-Pierre and Corthier, G\'{e}rard and Grangette, Corinne and Vasquez, Nadia and Pochart, Philippe and Seksik, Philippe and Langella, Philippe}, year={2008}, month={Oct}, pages={16731-16736}}

@article{Willing2009, title={Twin studies reveal specific imbalances in the mucosa-associated microbiota of patients with ileal Crohn's disease}, volume={15}, ISSN={1536-4844}, DOI={10.1002/ibd.20783},  note={00298}, number={5}, journal={Inflammatory Bowel Diseases}, author={Willing, Ben and Halfvarson, Jonas and Dicksved, Johan and Rosenquist, Magnus and J\"{a}rnerot, Gunnar and Engstrand, Lars and Tysk, Curt and Jansson, Janet K.}, year={2009}, month={May}, pages={653-660}}

@article{Willing2010, title={A Pyrosequencing Study in Twins Shows That Gastrointestinal Microbial Profiles Vary With Inflammatory Bowel Disease Phenotypes}, volume={139}, ISSN={0016-5085}, DOI={10.1053/j.gastro.2010.08.049},  note={00448}, number={6}, journal={Gastroenterology}, author={Willing, Ben P. and Dicksved, Johan and Halfvarson, Jonas and Andersson, Anders F. and Lucio, Marianna and Zheng, Zongli and J\"{a}rnerot, Gunnar and Tysk, Curt and Jansson, Janet K. and Engstrand, Lars}, year={2010}, month={Dec}, pages={1844-1854.e1}}

@article{Wills2014, title={Fecal Microbial Composition of Ulcerative Colitis and Crohn's Disease Patients in Remission and Subsequent Exacerbation}, volume={9}, ISSN={1932-6203}, url={http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3946581/}, DOI={10.1371/journal.pone.0090981},  note={00030}, number={3}, journal={PLoS ONE}, author={Wills, Edgar S. and Jonkers, Daisy M. A. E. and Savelkoul, Paul H. and Masclee, Ad A. and Pierik, Marieke J. and Penders, John}, year={2014}, month={Mar}}

@article{Young2013, title={Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis}, volume={1}, ISSN={2049-2618}, DOI={10.1186/2049-2618-1-9}, abstractNote={PMID: 24451366}, note={00016}, number={1}, journal={Microbiome}, author={Young, Vincent B. and Raffals, Laura H. and Huse, Susan M. and Vital, Marius and Dai, Dongjuan and Schloss, Patrick D. and Brulc, Jennifer M. and Antonopoulos, Dionysios A. and Arrieta, Rose L. and Kwon, John H. and Reddy, GAutham and Hubert, Nathaniel and Grim, Sharon and Vineis, Joseph and Dalal, Sushila and Morrison, Hilary and Eren, Murat and Meyer, Folker and Schmidt, Thomas and Tiedje, James and Chang, Eugene and Sogin, Mitch}, year={2013}, month={Mar}, pages={9}}

@article{Zaura2015, title={Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces}, volume={6}, ISSN={2150-7511}, DOI={10.1128/mBio.01693-15}, number={6}, journal={mBio}, author={Zaura, Egija and Brandt, Bernd W. and Teixeira de Mattos, M. Joost and Buijs, Mark J. and Caspers, Martien P. M. and Rashid, Mamun-Ur and Weintraub, Andrej and Nord, Carl Erik and Savell, Ann and Hu, Yanmin and Coates, Anthony and Hubank, Mike and Spratt, David and Wilson, Michael and Keijser, Bart and Crielaard, Wim}, year={2015}, pages={e01693-01615}}

@article{EMP2011,title={EMP DNA Extraction Protocol}, note={00000}, publisher={Earth Microbiome Project}, year={2011}}
 
 @article{RN41,
   author = {Backhed, F. and Ley, R. E. and Sonnenburg, J. L. and Peterson, D. A. and Gordon, J. I.},
   title = {Host-bacterial mutualism in the human intestine},
   journal = {Science},
   volume = {307},
   number = {5717},
   pages = {1915-20},
   ISSN = {1095-9203 (Electronic)
0036-8075 (Linking)},
   DOI = {10.1126/science.1104816},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15790844},
   year = {2005},
   type = {Journal Article}
}

@article{RN4221,
   author = {Caporaso, J. G. and Lauber, C. L. and Walters, W. A. and Berg-Lyons, D. and Huntley, J. and Fierer, N. and Owens, S. M. and Betley, J. and Fraser, L. and Bauer, M. and Gormley, N. and Gilbert, J. A. and Smith, G. and Knight, R.},
   title = {Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms},
   journal = {ISME J},
   volume = {6},
   number = {8},
   pages = {1621-4},
   ISSN = {1751-7370 (Electronic)
1751-7362 (Linking)},
   DOI = {10.1038/ismej.2012.8},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/22402401},
   year = {2012},
   type = {Journal Article}
}

@article{RN4235,
   author = {David, L. A. and Maurice, C. F. and Carmody, R. N. and Gootenberg, D. B. and Button, J. E. and Wolfe, B. E. and Ling, A. V. and Devlin, A. S. and Varma, Y. and Fischbach, M. A. and Biddinger, S. B. and Dutton, R. J. and Turnbaugh, P. J.},
   title = {Diet rapidly and reproducibly alters the human gut microbiome},
   journal = {Nature},
   volume = {505},
   number = {7484},
   pages = {559-63},
   ISSN = {1476-4687 (Electronic)
0028-0836 (Linking)},
   DOI = {10.1038/nature12820},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/24336217},
   year = {2014},
   type = {Journal Article}
}

@article{RN67,
   author = {Dethlefsen, L. and Relman, D. A.},
   title = {Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation},
   journal = {Proc Natl Acad Sci U S A},
   volume = {108 Suppl 1},
   pages = {4554-61},
   ISSN = {1091-6490 (Electronic)
0027-8424 (Linking)},
   DOI = {10.1073/pnas.1000087107},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20847294},
   year = {2011},
   type = {Journal Article}
}

@article{RN81,
   author = {Edgar, R. C.},
   title = {Search and clustering orders of magnitude faster than BLAST},
   journal = {Bioinformatics},
   volume = {26},
   number = {19},
   pages = {2460-1},
   ISSN = {1367-4811 (Electronic)
1367-4803 (Linking)},
   DOI = {10.1093/bioinformatics/btq461},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20709691},
   year = {2010},
   type = {Journal Article}
}

@article{RN84,
   author = {Faith, J. J. and Guruge, J. L. and Charbonneau, M. and Subramanian, S. and Seedorf, H. and Goodman, A. L. and Clemente, J. C. and Knight, R. and Heath, A. C. and Leibel, R. L. and Rosenbaum, M. and Gordon, J. I.},
   title = {The long-term stability of the human gut microbiota},
   journal = {Science},
   volume = {341},
   number = {6141},
   pages = {1237439},
   ISSN = {1095-9203 (Electronic)
0036-8075 (Linking)},
   DOI = {10.1126/science.1237439},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23828941},
   year = {2013},
   type = {Journal Article}
}

@article{RN53moviefmt,
   author = {Fuentes, S. and van Nood, E. and Tims, S. and Heikamp-de Jong, I. and ter Braak, C. J. and Keller, J. J. and Zoetendal, E. G. and de Vos, W. M.},
   title = {Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection},
   journal = {ISME J},
   volume = {8},
   number = {8},
   pages = {1621-33},
   ISSN = {1751-7370 (Electronic)
1751-7362 (Linking)},
   DOI = {10.1038/ismej.2014.13},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/24577353},
   year = {2014},
   type = {Journal Article}
}

@article{RN45,
   author = {Hamilton, M. J. and Weingarden, A. R. and Sadowsky, M. J. and Khoruts, A.},
   title = {Standardized frozen preparation for transplantation of fecal microbiota for recurrent Clostridium difficile infection},
   journal = {Am J Gastroenterol},
   volume = {107},
   number = {5},
   pages = {761-7},
   ISSN = {1572-0241 (Electronic)
0002-9270 (Linking)},
   DOI = {10.1038/ajg.2011.482},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22290405},
   year = {2012},
   type = {Journal Article}
}

@article{RN30,
   author = {Hamilton, M. J. and Weingarden, A. R. and Unno, T. and Khoruts, A. and Sadowsky, M. J.},
   title = {High-throughput DNA sequence analysis reveals stable engraftment of gut microbiota following transplantation of previously frozen fecal bacteria},
   journal = {Gut Microbes},
   volume = {4},
   number = {2},
   pages = {125-35},
   ISSN = {1949-0984 (Electronic)},
   DOI = {10.4161/gmic.23571},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23333862},
   year = {2013},
   type = {Journal Article}
}

@article{RN74,
   author = {Kawamoto, S. and Maruya, M. and Kato, L. M. and Suda, W. and Atarashi, K. and Doi, Y. and Tsutsui, Y. and Qin, H. and Honda, K. and Okada, T. and Hattori, M. and Fagarasan, S.},
   title = {Foxp3(+) T cells regulate immunoglobulin a selection and facilitate diversification of bacterial species responsible for immune homeostasis},
   journal = {Immunity},
   volume = {41},
   number = {1},
   pages = {152-65},
   ISSN = {1097-4180 (Electronic)
1074-7613 (Linking)},
   DOI = {10.1016/j.immuni.2014.05.016},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/25017466},
   year = {2014},
   type = {Journal Article}
}

@article{RN66,
   author = {Khoruts, A. and Dicksved, J. and Jansson, J. K. and Sadowsky, M. J.},
   title = {Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhea},
   journal = {J Clin Gastroenterol},
   volume = {44},
   number = {5},
   pages = {354-60},
   ISSN = {1539-2031 (Electronic)
0192-0790 (Linking)},
   DOI = {10.1097/MCG.0b013e3181c87e02},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20048681},
   year = {2010},
   type = {Journal Article}
}

@article{RN65,
   author = {Khoruts, A. and Weingarden, A. R.},
   title = {Emergence of fecal microbiota transplantation as an approach to repair disrupted microbial gut ecology},
   journal = {Immunol Lett},
   ISSN = {1879-0542 (Electronic)
0165-2478 (Linking)},
   DOI = {10.1016/j.imlet.2014.07.016},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/25106113},
   year = {2014},
   type = {Journal Article}
}

@article{RN3801,
   author = {Koren, O. and Goodrich, J. K. and Cullender, T. C. and Spor, A. and Laitinen, K. and Backhed, H. K. and Gonzalez, A. and Werner, J. J. and Angenent, L. T. and Knight, R. and Backhed, F. and Isolauri, E. and Salminen, S. and Ley, R. E.},
   title = {Host remodeling of the gut microbiome and metabolic changes during pregnancy},
   journal = {Cell},
   volume = {150},
   number = {3},
   pages = {470-80},
   ISSN = {1097-4172 (Electronic)
0092-8674 (Linking)},
   DOI = {10.1016/j.cell.2012.07.008},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22863002},
   year = {2012},
   type = {Journal Article}
}

@article{RN73,
   author = {Lozupone, C. A. and Li, M. and Campbell, T. B. and Flores, S. C. and Linderman, D. and Gebert, M. J. and Knight, R. and Fontenot, A. P. and Palmer, B. E.},
   title = {Alterations in the gut microbiota associated with HIV-1 infection},
   journal = {Cell Host Microbe},
   volume = {14},
   number = {3},
   pages = {329-39},
   ISSN = {1934-6069 (Electronic)
1931-3128 (Linking)},
   DOI = {10.1016/j.chom.2013.08.006},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/24034618},
   year = {2013},
   type = {Journal Article}
}

@article{RN83,
   author = {Lozupone, C. and Knight, R.},
   title = {UniFrac: a new phylogenetic method for comparing microbial communities},
   journal = {Appl Environ Microbiol},
   volume = {71},
   number = {12},
   pages = {8228-35},
   ISSN = {0099-2240 (Print)
0099-2240 (Linking)},
   DOI = {10.1128/AEM.71.12.8228-8235.2005},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16332807},
   year = {2005},
   type = {Journal Article}
}

@article{RN71,
   author = {Lupp, C. and Robertson, M. L. and Wickham, M. E. and Sekirov, I. and Champion, O. L. and Gaynor, E. C. and Finlay, B. B.},
   title = {Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae},
   journal = {Cell Host Microbe},
   volume = {2},
   number = {2},
   pages = {119-29},
   ISSN = {1934-6069 (Electronic)
1931-3128 (Linking)},
   DOI = {10.1016/j.chom.2007.06.010},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18005726},
   year = {2007},
   type = {Journal Article}
}

@article{RN3811,
   author = {McDonald, D. and Clemente, J. C. and Kuczynski, J. and Rideout, J. R. and Stombaugh, J. and Wendel, D. and Wilke, A. and Huse, S. and Hufnagle, J. and Meyer, F. and Knight, R. and Caporaso, J. G.},
   title = {The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome},
   journal = {Gigascience},
   volume = {1},
   number = {1},
   pages = {7},
   ISSN = {2047-217X (Electronic)
2047-217X (Linking)},
   DOI = {10.1186/2047-217X-1-7},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23587224},
   year = {2012},
   type = {Journal Article}
}

@article{RN31,
   author = {Seekatz, A. M. and Aas, J. and Gessert, C. E. and Rubin, T. A. and Saman, D. M. and Bakken, J. S. and Young, V. B.},
   title = {Recovery of the gut microbiome following fecal microbiota transplantation},
   journal = {MBio},
   volume = {5},
   number = {3},
   pages = {e00893-14},
   ISSN = {2150-7511 (Electronic)},
   DOI = {10.1128/mBio.00893-14},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/24939885},
   year = {2014},
   type = {Journal Article}
}

@article{RN36,
   author = {Shahinas, D. and Silverman, M. and Sittler, T. and Chiu, C. and Kim, P. and Allen-Vercoe, E. and Weese, S. and Wong, A. and Low, D. E. and Pillai, D. R.},
   title = {Toward an understanding of changes in diversity associated with fecal microbiome transplantation based on 16S rRNA gene deep sequencing},
   journal = {MBio},
   volume = {3},
   number = {5},
   ISSN = {2150-7511 (Electronic)},
   DOI = {10.1128/mBio.00338-12},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23093385},
   year = {2012},
   type = {Journal Article}
}

@article{RN35moviefmt,
   author = {Song, Y. and Garg, S. and Girotra, M. and Maddox, C. and von Rosenvinge, E. C. and Dutta, A. and Dutta, S. and Fricke, W. F.},
   title = {Microbiota dynamics in patients treated with fecal microbiota transplantation for recurrent Clostridium difficile infection},
   journal = {PLoS One},
   volume = {8},
   number = {11},
   pages = {e81330},
   ISSN = {1932-6203 (Electronic)
1932-6203 (Linking)},
   DOI = {10.1371/journal.pone.0081330},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/24303043},
   year = {2013},
   type = {Journal Article}
}

@article{RN79,
   author = {Vazquez-Baeza, Y. and Pirrung, M. and Gonzalez, A. and Knight, R.},
   title = {EMPeror: a tool for visualizing high-throughput microbial community data},
   journal = {Gigascience},
   volume = {2},
   number = {1},
   pages = {16},
   ISSN = {2047-217X (Electronic)
2047-217X (Linking)},
   DOI = {10.1186/2047-217X-2-16},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/24280061},
   year = {2013},
   type = {Journal Article}
}

@article{RN1,
   author = {Weingarden, A. R. and Chen, C. and Bobr, A. and Yao, D. and Lu, Y. and Nelson, V. M. and Sadowsky, M. J. and Khoruts, A.},
   title = {Microbiota transplantation restores normal fecal bile acid composition in recurrent Clostridium difficile infection},
   journal = {Am J Physiol Gastrointest Liver Physiol},
   volume = {306},
   number = {4},
   pages = {G310-9},
   ISSN = {1522-1547 (Electronic)
0193-1857 (Linking)},
   DOI = {10.1152/ajpgi.00282.2013},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/24284963},
   year = {2014},
   type = {Journal Article}
}

@article{RN26,
   author = {Youngster, I. and Sauk, J. and Pindar, C. and Wilson, R. G. and Kaplan, J. L. and Smith, M. B. and Alm, E. J. and Gevers, D. and Russell, G. H. and Hohmann, E. L.},
   title = {Fecal microbiota transplant for relapsing Clostridium difficile infection using a frozen inoculum from unrelated donors: a randomized, open-label, controlled pilot study},
   journal = {Clin Infect Dis},
   volume = {58},
   number = {11},
   pages = {1515-22},
   ISSN = {1537-6591 (Electronic)
1058-4838 (Linking)},
   DOI = {10.1093/cid/ciu135},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/24762631},
   year = {2014},
   type = {Journal Article}
}

@article{RN4225,
   author = {Montassier, E. and Al-Ghalith, G. A. and Ward, T. and Corvec, S. and Gastinne, T. and Potel, G. and Moreau, P. and de la Cochetiere, M. F. and Batard, E. and Knights, D.},
   title = {Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection},
   journal = {Genome Med},
   volume = {8},
   number = {1},
   pages = {49},
   ISSN = {1756-994X (Electronic)
1756-994X (Linking)},
   DOI = {10.1186/s13073-016-0301-4},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27121964},
   year = {2016},
   type = {Journal Article}
}

@article{RN4226,
   author = {Nakayama, H. and Okumichi, T. and Nakashima, S. and Kimura, A. and Ikeda, M. and Kajihara, H.},
   title = {Papillary adenocarcinoma of the sigmoid colon associated with psammoma bodies and hyaline globules: report of a case},
   journal = {Jpn J Clin Oncol},
   volume = {27},
   number = {3},
   pages = {193-6},
   ISSN = {0368-2811 (Print)
0368-2811 (Linking)},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/9255277},
   year = {1997},
   type = {Journal Article}
}


@article{RN1490,
   author = {Faith, D. P.},
   title = {Phylogenetic diversity, functional trait diversity and extinction: avoiding tipping points and worst-case losses},
   journal = {Philos Trans R Soc Lond B Biol Sci},
   volume = {370},
   number = {1662},
   pages = {20140011},
   ISSN = {1471-2970 (Electronic)
0962-8436 (Linking)},
   DOI = {10.1098/rstb.2014.0011},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/25561672},
   year = {2015},
   type = {Journal Article}
}

@article{RN1515,
   author = {Halfvarson, J. and Brislawn, C. J. and Lamendella, R. and Vazquez-Baeza, Y. and Walters, W. A. and Bramer, L. M. and D'Amato, M. and Bonfiglio, F. and McDonald, D. and Gonzalez, A. and McClure, E. E. and Dunklebarger, M. F. and Knight, R. and Jansson, J. K.},
   title = {Dynamics of the human gut microbiome in inflammatory bowel disease},
   journal = {Nat Microbiol},
   volume = {2}, 
   pages = {17004},
   ISSN = {2058-5276 (Electronic)
2058-5276 (Linking)},
   DOI = {10.1038/nmicrobiol.2017.4},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28191884},
   year = {2017},
   type = {Journal Article}
}

@article{RN1516,
   author = {Jones, E. and Oliphant, E  and Peterson, P. and The SciPy Development Team},
   title = {SciPy: Open Source Scientific Tools for Python, 2001--, http://www.scipy.org/ [Online; accessed 2017-04-06]},
   type = {Journal Article}
}

@article{RN1484,
   author = {Kelly, C. R. and Kahn, S. and Kashyap, P. and Laine, L. and Rubin, D. and Atreja, A. and Moore, T. and Wu, G.},
   title = {Update on Fecal Microbiota Transplantation 2015: Indications, Methodologies, Mechanisms, and Outlook},
   journal = {Gastroenterology},
   volume = {149},
   number = {1},
   pages = {223-37},
   ISSN = {1528-0012 (Electronic)
0016-5085 (Linking)},
   DOI = {10.1053/j.gastro.2015.05.008},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/25982290},
   year = {2015},
   type = {Journal Article}
}

@article{RN1527,
   author = {Kelly, C. R. and Khoruts, A. and Staley, C. and Sadowsky, M. J. and Abd, M. and Alani, M. and Bakow, B. and Curran, P. and McKenney, J. and Tisch, A. and Reinert, S. E. and Machan, J. T. and Brandt, L. J.},
   title = {Effect of Fecal Microbiota Transplantation on Recurrence in Multiply Recurrent Clostridium difficile Infection: A Randomized Trial},
   journal = {Ann Intern Med},
   volume = {165},
   number = {9},
   pages = {609-616},
   ISSN = {1539-3704 (Electronic)
0003-4819 (Linking)},
   DOI = {10.7326/M16-0271},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27547925},
   year = {2016},
   type = {Journal Article}
}

@article{RN1498,
   author = {Khanna, S.  and Weatherly, R. and Kammer, P. P.  and Pardi, D.S.},
   title = {Management and Outcomes of Patients With Failed Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection},
   journal = {Am J Gastroenterol},
   volume = {110},
   pages = {S580},
   year = {2015},
   type = {Journal Article}
}

@article{RN1446,
   author = {Khanna, S. and Pardi, D. S.},
   title = {Clostridium difficile infection: management strategies for a difficult disease},
   journal = {Therap Adv Gastroenterol},
   volume = {7},
   number = {2},
   pages = {72-86},
   ISSN = {1756-283X (Print)
1756-283X (Linking)},
   DOI = {10.1177/1756283X13508519},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/24587820},
   year = {2014},
   type = {Journal Article}
}

@article{RN1480,
   author = {Khanna, S. and Pardi, D. S.},
   title = {Clinical implications of antibiotic impact on gastrointestinal microbiota and Clostridium difficile infection},
   journal = {Expert Rev Gastroenterol Hepatol},
   pages = {1-8},
   ISSN = {1747-4132 (Electronic)
1747-4124 (Linking)},
   DOI = {10.1586/17474124.2016.1158097},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/26907220},
   year = {2016},
   type = {Journal Article}
}

@article{RN1479,
   author = {Khanna, S. and Pardi, D. S. and Kelly, C. R. and Kraft, C. S. and Dhere, T. and Henn, M. R. and Lombardo, M. J. and Vulic, M. and Ohsumi, T. and Winkler, J. and Pindar, C. and McGovern, B. H. and Pomerantz, R. J. and Aunins, J. G. and Cook, D. N. and Hohmann, E. L.},
   title = {A Novel Microbiome Therapeutic Increases Gut Microbial Diversity and Prevents Recurrent Clostridium difficile Infection},
   journal = {J Infect Dis},
   ISSN = {1537-6613 (Electronic)
0022-1899 (Linking)},
   DOI = {10.1093/infdis/jiv766},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/26908752},
   year = {2016},
   type = {Journal Article}
}

@article{RN1477,
   author = {Khanna, S. and Tosh, P. K.},
   title = {A clinician's primer on the role of the microbiome in human health and disease},
   journal = {Mayo Clin Proc},
   volume = {89},
   number = {1},
   pages = {107-14},
   ISSN = {1942-5546 (Electronic)
0025-6196 (Linking)},
   DOI = {10.1016/j.mayocp.2013.10.011},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/24388028},
   year = {2014},
   type = {Journal Article}
}

@article{RN1497,
   author = {Khoruts, A. and Rank, K. M. and Newman, K. M. and Viskocil, K. and Vaughn, B. P. and Hamilton, M. J. and Sadowsky, M. J.},
   title = {Inflammatory Bowel Disease Affects the Outcome of Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection},
   journal = {Clin Gastroenterol Hepatol},
   ISSN = {1542-7714 (Electronic)
1542-3565 (Linking)},
   DOI = {10.1016/j.cgh.2016.02.018},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/26905904},
   year = {2016},
   type = {Journal Article}
}

@article{RN3995,
   author = {Knights, D. and Kuczynski, J. and Charlson, E. S. and Zaneveld, J. and Mozer, M. C. and Collman, R. G. and Bushman, F. D. and Knight, R. and Kelley, S. T.},
   title = {Bayesian community-wide culture-independent microbial source tracking},
   journal = {Nat Methods},
   volume = {8},
   number = {9},
   pages = {761-3},
   ISSN = {1548-7105 (Electronic)
1548-7091 (Linking)},
   DOI = {10.1038/nmeth.1650},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21765408},
   year = {2011},
   type = {Journal Article}
}

@article{RN3810,
   author = {Kopylova, E. and Noe, L. and Touzet, H.},
   title = {SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data},
   journal = {Bioinformatics},
   volume = {28},
   number = {24},
   pages = {3211-7},
   ISSN = {1367-4811 (Electronic)
1367-4803 (Linking)},
   DOI = {10.1093/bioinformatics/bts611},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23071270},
   year = {2012},
   type = {Journal Article}
}

@article{RN1478,
   author = {Lessa, F. C. and Winston, L. G. and McDonald, L. C. and Emerging Infections Program, C. difficile Surveillance Team},
   title = {Burden of Clostridium difficile infection in the United States},
   journal = {N Engl J Med},
   volume = {372},
   number = {24},
   pages = {2369-70},
   ISSN = {1533-4406 (Electronic)
0028-4793 (Linking)},
   DOI = {10.1056/NEJMc1505190},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/26061850},
   year = {2015},
   type = {Journal Article}
}

@article{RN1513,
   author = {Mandal, S. and Van Treuren, W. and White, R. A. and Eggesbo, M. and Knight, R. and Peddada, S. D.},
   title = {Analysis of composition of microbiomes: a novel method for studying microbial composition},
   journal = {Microb Ecol Health Dis},
   volume = {26},
   pages = {27663},
   ISSN = {0891-060X (Print)
0891-060X (Linking)},
   DOI = {10.3402/mehd.v26.27663},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/26028277},
   year = {2015},
   type = {Journal Article}
}

@article{RN3982,
   author = {Moayyedi, P. and Surette, M. G. and Kim, P. T. and Libertucci, J. and Wolfe, M. and Onischi, C. and Armstrong, D. and Marshall, J. K. and Kassam, Z. and Reinisch, W. and Lee, C. H.},
   title = {Fecal Microbiota Transplantation Induces Remission in Patients With Active Ulcerative Colitis in a Randomized Controlled Trial},
   journal = {Gastroenterology},
   volume = {149},
   number = {1},
   pages = {102-109 e6},
   ISSN = {1528-0012 (Electronic)
0016-5085 (Linking)},
   DOI = {10.1053/j.gastro.2015.04.001},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/25857665},
   year = {2015},
   type = {Journal Article}
}

@article{RN1481,
   author = {Orenstein, R. and Dubberke, E. and Hardi, R. and Ray, A. and Mullane, K. and Pardi, D. S. and Ramesh, M. S. and Investigators, Punch Cd},
   title = {Safety and Durability of RBX2660 (Microbiota Suspension) for Recurrent Clostridium difficile Infection: Results of the PUNCH CD Study},
   journal = {Clin Infect Dis},
   volume = {62},
   number = {5},
   pages = {596-602},
   ISSN = {1537-6591 (Electronic)
1058-4838 (Linking)},
   DOI = {10.1093/cid/civ938},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/26565008},
   year = {2016},
   type = {Journal Article}
}

@article{RN1019,
   author = {Paramsothy, S. and Kamm, M. A. and Kaakoush, N. O. and Walsh, A. J. and van den Bogaerde, J. and Samuel, D. and Leong, R. W. and Connor, S. and Ng, W. and Paramsothy, R. and Xuan, W. and Lin, E. and Mitchell, H. M. and Borody, T. J.},
   title = {Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial},
   journal = {Lancet},
   ISSN = {1474-547X (Electronic)
0140-6736 (Linking)},
   DOI = {10.1016/S0140-6736(17)30182-4},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28214091},
   year = {2017},
   type = {Journal Article}
}

@article{RN1483,
   author = {Rossen, N. G. and Fuentes, S. and van der Spek, M. J. and Tijssen, J. G. and Hartman, J. H. and Duflou, A. and Lowenberg, M. and van den Brink, G. R. and Mathus-Vliegen, E. M. and de Vos, W. M. and Zoetendal, E. G. and D'Haens, G. R. and Ponsioen, C. Y.},
   title = {Findings From a Randomized Controlled Trial of Fecal Transplantation for Patients With Ulcerative Colitis},
   journal = {Gastroenterology},
   volume = {149},
   number = {1},
   pages = {110-118 e4},
   ISSN = {1528-0012 (Electronic)
0016-5085 (Linking)},
   DOI = {10.1053/j.gastro.2015.03.045},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/25836986},
   year = {2015},
   type = {Journal Article}
}

@article{RN1524,
   author = {Staley, C. and Kelly, C. R. and Brandt, L. J. and Khoruts, A. and Sadowsky, M. J.},
   title = {Complete Microbiota Engraftment Is Not Essential for Recovery from Recurrent Clostridium difficile Infection following Fecal Microbiota Transplantation},
   journal = {MBio},
   volume = {7},
   number = {6},
   ISSN = {2150-7511 (Electronic)},
   DOI = {10.1128/mBio.01965-16},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27999162},
   year = {2016},
   type = {Journal Article}
}

@article{RN1523,
   author = {Tariq, R. and Weatherly, R. and Kammer, P. and Pardi, D. S. and Khanna, S.},
   title = {Donor Screening Experience for Fecal Microbiota Transplantation in Patients With Recurrent C. difficile Infection},
   journal = {J Clin Gastroenterol},
   ISSN = {1539-2031 (Electronic)
0192-0790 (Linking)},
   DOI = {10.1097/MCG.0000000000000768},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27984397},
   year = {2016},
   type = {Journal Article}
}

@article{RN1471,
   author = {Weingarden, A. and Gonzalez, A. and Vazquez-Baeza, Y. and Weiss, S. and Humphry, G. and Berg-Lyons, D. and Knights, D. and Unno, T. and Bobr, A. and Kang, J. and Khoruts, A. and Knight, R. and Sadowsky, M. J.},
   title = {Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection},
   journal = {Microbiome},
   volume = {3},
   pages = {10},
   ISSN = {2049-2618 (Electronic)
2049-2618 (Linking)},
   DOI = {10.1186/s40168-015-0070-0},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/25825673},
   year = {2015},
   type = {Journal Article}
}

@article{RN4220,
   author = {Costello, E. K. and Lauber, C. L. and Hamady, M. and Fierer, N. and Gordon, J. I. and Knight, R.},
   title = {Bacterial community variation in human body habitats across space and time},
   journal = {Science},
   volume = {326},
   number = {5960},
   pages = {1694-7},
   ISSN = {1095-9203 (Electronic)
0036-8075 (Linking)},
   DOI = {10.1126/science.1177486},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/19892944},
   year = {2009},
   type = {Journal Article}
}

@article{RN4017,
   author = {Hartigan, J. A. and Hartigan, P. M.},
   title = {The Dip Test of Unimodality},
   pages = {70-84},
   ISSN = {0090-5364},
   DOI = {10.1214/aos/1176346577},
   url = {http://projecteuclid.org/euclid.aos/1176346577},
   year = {1985},
   type = {Journal Article}
}

@article{RN4222,
   author = {Liu, Z. and DeSantis, T. Z. and Andersen, G. L. and Knight, R.},
   title = {Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers},
   journal = {Nucleic Acids Res},
   volume = {36},
   number = {18},
   pages = {e120},
   ISSN = {1362-4962 (Electronic)
0305-1048 (Linking)},
   DOI = {10.1093/nar/gkn491},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/18723574},
   year = {2008},
   type = {Journal Article}
}

@article{RN4006,
   author = {Thia, K. and Faubion, W. A., Jr. and Loftus, E. V., Jr. and Persson, T. and Persson, A. and Sandborn, W. J.},
   title = {Short CDAI: development and validation of a shortened and simplified Crohn's disease activity index},
   journal = {Inflamm Bowel Dis},
   volume = {17},
   number = {1},
   pages = {105-11},
   ISSN = {1536-4844 (Electronic)
1078-0998 (Linking)},
   DOI = {10.1002/ibd.21400},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20629100},
   year = {2011},
   type = {Journal Article}
}

@article {GalloSkin,
  author = {Nakatsuji, Teruaki and Chen, Tiffany H. and Narala, Saisindhu and Chun, Kimberly A. and Two, Aimee M. and Yun, Tong and Shafiq, Faiza and Kotol, Paul F. and Bouslimani, Amina and Melnik, Alexey V. and Latif, Haythem and Kim, Ji-Nu and Lockhart, Alexandre and Artis, Keli and David, Gloria and Taylor, Patricia and Streib, Joanne and Dorrestein, Pieter C. and Grier, Alex and Gill, Steven R. and Zengler, Karsten and Hata, Tissa R. and Leung, Donald Y. M. and Gallo, Richard L.},
  title = {Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis},
  volume = {9},
  number = {378},
  year = {2017},
  doi = {10.1126/scitranslmed.aah4680},
  publisher = {American Association for the Advancement of Science},
  abstract = {Normal human skin is colonized by a variety of bacteria, which typically do not perturb the host. However, Staphylococcus aureus is known to aggravate symptoms of atopic dermatitis. Nakatsuji et al. report that other strains of Staphylococcus residing on the skin of healthy individuals produce a novel antimicrobial peptide that can inhibit S. aureus growth. Colonization of pigskin or mice with these protective commensals reduced S. aureus replication. Autologous bacterial transplant in a small number of atopic dermatitis patients drastically reduced S. aureus skin burden. This commensal skin transplant is already approved by the U.S. Food and Drug Administration, with a clinical trial underway.The microbiome can promote or disrupt human health by influencing both adaptive and innate immune functions. We tested whether bacteria that normally reside on human skin participate in host defense by killing Staphylococcus aureus, a pathogen commonly found in patients with atopic dermatitis (AD) and an important factor that exacerbates this disease. High-throughput screening for antimicrobial activity against S. aureus was performed on isolates of coagulase-negative Staphylococcus (CoNS) collected from the skin of healthy and AD subjects. CoNS strains with antimicrobial activity were common on the normal population but rare on AD subjects. A low frequency of strains with antimicrobial activity correlated with colonization by S. aureus. The antimicrobial activity was identified as previously unknown antimicrobial peptides (AMPs) produced by CoNS species including Staphylococcus epidermidis and Staphylococcus hominis. These AMPs were strain-specific, highly potent, selectively killed S. aureus, and synergized with the human AMP LL-37. Application of these CoNS strains to mice confirmed their defense function in vivo relative to application of nonactive strains. Strikingly, reintroduction of antimicrobial CoNS strains to human subjects with AD decreased colonization by S. aureus. These findings show how commensal skin bacteria protect against pathogens and demonstrate how dysbiosis of the skin microbiome can lead to disease.},
  issn = {1946-6234},
  URL = {http://stm.sciencemag.org/content/9/378/eaah4680},
  eprint = {http://stm.sciencemag.org/content/9/378/eaah4680.full.pdf},
  journal = {Science Translational Medicine}
}