TY - JOUR AU - Ahern, P. P. AU - Faith, J. J. AU - Gordon, J. I. PY - 2014 DA - 2014// TI - Mining the human gut microbiota for effector strains that shape the immune system JO - Immunity VL - 40 UR - https://doi.org/10.1016/j.immuni.2014.05.012 DO - 10.1016/j.immuni.2014.05.012 ID - Ahern2014 ER - TY - JOUR AU - Round, J. L. AU - Mazmanian, S. K. PY - 2009 DA - 2009// TI - The gut microbiota shapes intestinal immune responses during health and disease JO - Nat Rev Immunol VL - 9 UR - https://doi.org/10.1038/nri2515 DO - 10.1038/nri2515 ID - Round2009 ER - TY - JOUR AU - Sekirov, I. AU - Russell, S. L. AU - Antunes, L. C. AU - Finlay, B. B. PY - 2010 DA - 2010// TI - Gut microbiota in health and disease JO - Physiol Rev VL - 90 UR - https://doi.org/10.1152/physrev.00045.2009 DO - 10.1152/physrev.00045.2009 ID - Sekirov2010 ER - TY - JOUR AU - Wolf, K. J. AU - Daft, J. G. AU - Tanner, S. M. AU - Hartmann, R. AU - Khafipour, E. AU - Lorenz, R. G. PY - 2014 DA - 2014// TI - Consumption of acidic water alters the gut microbiome and decreases the risk of diabetes in NOD mice JO - J Histochem Cytochem VL - 62 UR - https://doi.org/10.1369/0022155413519650 DO - 10.1369/0022155413519650 ID - Wolf2014 ER - TY - JOUR AU - Giongo, A. AU - Gano, K. A. AU - Crabb, D. B. AU - Mukherjee, N. AU - Novelo, L. L. AU - Casella, G. PY - 2011 DA - 2011// TI - Toward defining the autoimmune microbiome for type 1 diabetes JO - ISME J VL - 5 UR - https://doi.org/10.1038/ismej.2010.92 DO - 10.1038/ismej.2010.92 ID - Giongo2011 ER - TY - CHAP AU - Suzuki, T. AU - Yamada, T. AU - Fujimura, T. AU - Kawamura, E. AU - Shimizu, M. AU - Yamashita, R. ED - Rygaard, J. ED - Brunner, N. ED - Graem, N. ED - Spang-Thomsen, M. PY - 1987 DA - 1987// TI - Diabetogenic effects of lymphocyte transfusion on the NOD or NOD nude mouse. Pp. 112-116 BT - Immune-deficient animals in biomedical research PB - Karger CY - Basel ID - Suzuki1987 ER - TY - JOUR AU - Duck, L. W. AU - Walter, M. R. AU - Novak, J. AU - Kelly, D. AU - Tomasi, M. AU - Cong, Y. PY - 2007 DA - 2007// TI - Isolation of flagellated bacteria implicated in Crohn’s disease JO - Inflamm Bowel Dis VL - 13 UR - https://doi.org/10.1002/ibd.20237 DO - 10.1002/ibd.20237 ID - Duck2007 ER - TY - JOUR AU - Manichanh, C. AU - Borruel, N. AU - Casellas, F. AU - Guarner, F. PY - 2012 DA - 2012// TI - The gut microbiota in IBD JO - Nat Rev Gastroenterol Hepatol VL - 9 UR - https://doi.org/10.1038/nrgastro.2012.152 DO - 10.1038/nrgastro.2012.152 ID - Manichanh2012 ER - TY - JOUR AU - Hildebrand, F. AU - Nguyen, T. L. AU - Brinkman, B. AU - Yunta, R. G. AU - Cauwe, B. AU - Vandenabeele, P. PY - 2013 DA - 2013// TI - Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice JO - Genome Biol VL - 14 UR - https://doi.org/10.1186/gb-2013-14-1-r4 DO - 10.1186/gb-2013-14-1-r4 ID - Hildebrand2013 ER - TY - JOUR AU - Garrett, W. S. AU - Lord, G. M. AU - Punit, S. AU - Lugo-Villarino, G. AU - Mazmanian, S. K. AU - Ito, S. PY - 2007 DA - 2007// TI - Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system JO - Cell VL - 131 UR - https://doi.org/10.1016/j.cell.2007.08.017 DO - 10.1016/j.cell.2007.08.017 ID - Garrett2007 ER - TY - STD TI - Peng J, Narasimhan S, Marchesi JR, Benson A, Wong FS, Wen L. Long term effect of gut microbiota transfer on diabetes development. J Autoimmun. 2014. doi:10.1016/j.jaut.2014.03.005 ID - ref11 ER - TY - JOUR AU - David, L. A. AU - Maurice, C. F. AU - Carmody, R. N. AU - Gootenberg, D. B. AU - Button, J. E. AU - Wolfe, B. E. PY - 2014 DA - 2014// TI - Diet rapidly and reproducibly alters the human gut microbiome JO - Nature VL - 505 UR - https://doi.org/10.1038/nature12820 DO - 10.1038/nature12820 ID - David2014 ER - TY - JOUR AU - Hansen, C. H. AU - Krych, L. AU - Nielsen, D. S. AU - Vogensen, F. K. AU - Hansen, L. H. AU - Sorensen, S. J. PY - 2012 DA - 2012// TI - Early life treatment with vancomycin propagates Akkermansia muciniphila and reduces diabetes incidence in the NOD mouse JO - Diabetologia VL - 55 UR - https://doi.org/10.1007/s00125-012-2564-7 DO - 10.1007/s00125-012-2564-7 ID - Hansen2012 ER - TY - JOUR AU - Schwartz, R. F. AU - Neu, J. AU - Schatz, D. AU - Atkinson, M. A. AU - Wasserfall, C. PY - 2007 DA - 2007// TI - Comment on: Brugman S et al. (2006) Antibiotic treatment partially protects against type 1 diabetes in the Bio-Breeding diabetes-prone rat. Is the gut flora involved in the development of type 1 diabetes? Diabetologia 49:2105–2108 JO - Diabetologia VL - 50 UR - https://doi.org/10.1007/s00125-006-0526-7 DO - 10.1007/s00125-006-0526-7 ID - Schwartz2007 ER - TY - JOUR AU - Goodrich, J. K. AU - Rienzi, S. C. AU - Poole, A. C. AU - Koren, O. AU - Walters, W. A. AU - Caporaso, J. G. PY - 2014 DA - 2014// TI - Conducting a microbiome study JO - Cell VL - 158 UR - https://doi.org/10.1016/j.cell.2014.06.037 DO - 10.1016/j.cell.2014.06.037 ID - Goodrich2014 ER - TY - JOUR AU - Thoene-Reineke, C. AU - Fischer, A. AU - Friese, C. AU - Briesemeister, D. AU - Gobel, U. B. AU - Kammertoens, T. PY - 2014 DA - 2014// TI - Composition of intestinal microbiota in immune-deficient mice kept in three different housing conditions JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0113406 DO - 10.1371/journal.pone.0113406 ID - Thoene-Reineke2014 ER - TY - JOUR AU - Rogers, G. B. AU - Kozlowska, J. AU - Keeble, J. AU - Metcalfe, K. AU - Fao, M. AU - Dowd, S. E. PY - 2014 DA - 2014// TI - Functional divergence in gastrointestinal microbiota in physically-separated genetically identical mice JO - Sci Rep VL - 4 UR - https://doi.org/10.1038/srep05437 DO - 10.1038/srep05437 ID - Rogers2014 ER - TY - JOUR AU - Ubeda, C. AU - Lipuma, L. AU - Gobourne, A. AU - Viale, A. AU - Leiner, I. AU - Equinda, M. PY - 2012 DA - 2012// TI - Familial transmission rather than defective innate immunity shapes the distinct intestinal microbiota of TLR-deficient mice JO - J Exp Med VL - 209 UR - https://doi.org/10.1084/jem.20120504 DO - 10.1084/jem.20120504 ID - Ubeda2012 ER - TY - JOUR AU - Wen, L. AU - Ley, R. E. AU - Volchkov, P. Y. AU - Stranges, P. B. AU - Avanesyan, L. AU - Stonebraker, A. C. PY - 2008 DA - 2008// TI - Innate immunity and intestinal microbiota in the development of Type 1 diabetes JO - Nature VL - 455 UR - https://doi.org/10.1038/nature07336 DO - 10.1038/nature07336 ID - Wen2008 ER - TY - STD TI - Seekatz AM, Aas J, Gessert CE, Rubin TA, Saman DM, Bakken JS, et al. Recovery of the gut microbiome following fecal microbiota transplantation. MBio. 2014;5(3). doi:10.1128/mBio.00893-14. ID - ref20 ER - TY - JOUR AU - Borody, T. J. AU - Paramsothy, S. AU - Agrawal, G. PY - 2013 DA - 2013// TI - Fecal microbiota transplantation: indications, methods, evidence, and future directions JO - Curr Gastroenterol Rep VL - 15 UR - https://doi.org/10.1007/s11894-013-0337-1 DO - 10.1007/s11894-013-0337-1 ID - Borody2013 ER - TY - JOUR AU - Smits, L. P. AU - Bouter, K. E. AU - Vos, W. M. AU - Borody, T. J. AU - Nieuwdorp, M. PY - 2013 DA - 2013// TI - Therapeutic potential of fecal microbiota transplantation JO - Gastroenterology VL - 145 UR - https://doi.org/10.1053/j.gastro.2013.08.058 DO - 10.1053/j.gastro.2013.08.058 ID - Smits2013 ER - TY - JOUR AU - Markle, J. G. AU - Frank, D. N. AU - Mortin-Toth, S. AU - Robertson, C. E. AU - Feazel, L. M. AU - Rolle-Kampczyk, U. PY - 2013 DA - 2013// TI - Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity JO - Science VL - 339 UR - https://doi.org/10.1126/science.1233521 DO - 10.1126/science.1233521 ID - Markle2013 ER - TY - STD TI - Hansen CH, Andersen LS, Krych L, Metzdorff SB, Hasselby JP, Skov S, et al. Mode of delivery shapes gut colonization pattern and modulates regulatory immunity in mice. J Immunol. 2014. doi:10.4049/jimmunol.1400085 ID - ref24 ER - TY - JOUR AU - Murri, M. AU - Leiva, I. AU - Gomez-Zumaquero, J. M. AU - Tinahones, F. J. AU - Cardona, F. AU - Soriguer, F. PY - 2013 DA - 2013// TI - Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case–control study JO - BMC Med VL - 11 UR - https://doi.org/10.1186/1741-7015-11-46 DO - 10.1186/1741-7015-11-46 ID - Murri2013 ER - TY - JOUR AU - Chen, W. AU - Liu, F. AU - Ling, Z. AU - Tong, X. AU - Xiang, C. PY - 2012 DA - 2012// TI - Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0039743 DO - 10.1371/journal.pone.0039743 ID - Chen2012 ER - TY - JOUR AU - Willing, B. P. AU - Dicksved, J. AU - Halfvarson, J. AU - Andersson, A. F. AU - Lucio, M. AU - Zheng, Z. PY - 2010 DA - 2010// TI - A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes JO - Gastroenterology VL - 139 UR - https://doi.org/10.1053/j.gastro.2010.08.049 DO - 10.1053/j.gastro.2010.08.049 ID - Willing2010 ER - TY - STD TI - Bolotin A, de Wouters T, Schnupf P, Bouchier C, Loux V, Rhimi M, et al. Genome Sequence of “Candidatus Arthromitus” sp. Strain SFB-Mouse-NL, a commensal bacterium with a key role in postnatal maturation of gut immune functions. Genome Announc. 2014;2(4). doi:10.1128/genomeA.00705-14. ID - ref28 ER - TY - JOUR AU - Thompson, C. L. AU - Vier, R. AU - Mikaelyan, A. AU - Wienemann, T. AU - Brune, A. PY - 2012 DA - 2012// TI - ‘Candidatus Arthromitus’ revised: segmented filamentous bacteria in arthropod guts are members of Lachnospiraceae JO - Environ Microbiol VL - 14 UR - https://doi.org/10.1111/j.1462-2920.2012.02731.x DO - 10.1111/j.1462-2920.2012.02731.x ID - Thompson2012 ER - TY - JOUR AU - Kriegel, M. A. AU - Sefik, E. AU - Hill, J. A. AU - Wu, H. J. AU - Benoist, C. AU - Mathis, D. PY - 2011 DA - 2011// TI - Naturally transmitted segmented filamentous bacteria segregate with diabetes protection in nonobese diabetic mice JO - Proc Natl Acad Sci U S A VL - 108 UR - https://doi.org/10.1073/pnas.1108924108 DO - 10.1073/pnas.1108924108 ID - Kriegel2011 ER - TY - JOUR AU - Kumar, R. AU - Eipers, P. AU - Little, R. B. AU - Crowley, M. AU - Crossman, D. K. AU - Lefkowitz, E. J. PY - 2014 DA - 2014// TI - Getting started with microbiome analysis: sample acquisition to bioinformatics JO - Curr Protoc Hum Genet VL - 82 UR - https://doi.org/10.1002/0471142905.hg1808s82 DO - 10.1002/0471142905.hg1808s82 ID - Kumar2014 ER - TY - JOUR AU - Edgar, R. C. PY - 2010 DA - 2010// TI - Search and clustering orders of magnitude faster than BLAST JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq461 DO - 10.1093/bioinformatics/btq461 ID - Edgar2010 ER - TY - JOUR AU - Lozupone, C. A. AU - Hamady, M. AU - Kelley, S. T. AU - Knight, R. PY - 2007 DA - 2007// TI - Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities JO - Appl Environ Microbiol VL - 73 UR - https://doi.org/10.1128/AEM.01996-06 DO - 10.1128/AEM.01996-06 ID - Lozupone2007 ER - TY - JOUR AU - Navas-Molina, J. A. AU - Peralta-Sanchez, J. M. AU - Gonzalez, A. AU - McMurdie, P. J. AU - Vazquez-Baeza, Y. AU - Xu, Z. PY - 2013 DA - 2013// TI - Advancing our understanding of the human microbiome using QIIME JO - Methods Enzymol VL - 531 UR - https://doi.org/10.1016/B978-0-12-407863-5.00019-8 DO - 10.1016/B978-0-12-407863-5.00019-8 ID - Navas-Molina2013 ER -