Các kiểu enterotype liên quan đến viêm nhiễm, kiểu gen chủ thể, ảnh hưởng từ chuồng nuôi và cá nhân góp phần vào sự biến thiên của vi khuẩn đường ruột ở chuột thí nghiệm thông dụng

Genome Biology - Tập 14 - Trang 1-15 - 2013
Falk Hildebrand1,2, Thi Loan Anh Nguyen1,2,3,4, Brigitta Brinkman5,6, Roberto Garcia Yunta1,2, Benedicte Cauwe3, Peter Vandenabeele5,6, Adrian Liston3,4, Jeroen Raes1,2
1Department of Structural Biology, VIB, 1050, Belgium
2Department of Bioscience Engineering, Vrije Universiteit Brussel, Brussels, Belgium
3Autoimmune Genetics Laboratory, Leuven, Belgium
4Katholieke Universiteit Leuven, Leuven, Belgium
5Department for Molecular Biomedical Research, Ghent, Belgium
6Department for Molecular Biomedical Research, GhentUniversity, Ghent, Belgium

Tóm tắt

Các mô hình chuột là thành phần thiết yếu trong nghiên cứu vi khuẩn đường ruột. Thật không may, sự đa dạng về di truyền và thiết lập thí nghiệm, cùng với những biến thiên giữa các cá nhân, đã làm phức tạp việc so sánh giữa các nghiên cứu và hiểu biết toàn cầu về cảnh quan vi khuẩn của chuột. Ở đây, chúng tôi khảo sát sự biến thiên của vi khuẩn đường ruột ở chuột khỏe mạnh thuộc năm dòng chuột thí nghiệm phổ biến bằng cách sử dụng phương pháp pyrosequencing 16S rDNA. Chúng tôi phát hiện bằng chứng ban đầu cho thấy sự phong phú có động lực, không phụ thuộc vào dòng chuột, dẫn đến các kiểu enterotype ở chuột có sự tương đồng rõ rệt với những kiểu ở con người, và những kiểu này liên quan đến mức độ calprotectin, một dấu hiệu của viêm ruột. Sau khi phân loại theo enterotype, chúng tôi nhận thấy rằng biến số di truyền, ảnh hưởng từ chuồng nuôi và biến thiên giữa các cá nhân đóng góp trung bình lần lượt là 19%, 31.7% và 45.5% vào biến thiên trong thành phần vi khuẩn đường ruột của chuột. Khoảng cách di truyền có tương quan tích cực với khoảng cách vi khuẩn, vì vậy các dòng chuột có di truyền tương đồng có vi khuẩn tương đồng hơn so với các dòng có di truyền xa nhau. Một số dòng chuột nhất định được làm giàu cho các đơn vị thuế học và nhóm thuế học cụ thể, trong khi hiệu ứng "chuồng nuôi" có thể xảy ra trên các ranh giới dòng chuột và chủ yếu được điều khiển bởi nhiễm trùng Helicobacter. Việc phát hiện các kiểu enterotype gợi ý một nguyên nhân sinh thái chung, có thể là viêm mức độ nhẹ có thể thúc đẩy sự khác biệt giữa thành phần vi khuẩn đường ruột ở động vật có vú. Hơn nữa, các hiệu ứng môi trường và di truyền được quan sát có những hậu quả quan trọng cho thiết kế thí nghiệm trong nghiên cứu vi khuẩn đường ruột ở chuột.

Từ khóa

#vi khuẩn đường ruột #enterotype #chuột thí nghiệm #di truyền #viêm nhiễm

Tài liệu tham khảo

Khachatryan ZA, Ktsoyan ZA, Manukyan GP, Kelly D, Ghazaryan KA, Aminov RI: Predominant role of host genetics in controlling the composition of gut microbiota. PLoS One. 2008, 3: e3064-10.1371/journal.pone.0003064.

Frank DN, Robertson CE, Hamm CM, Kpadeh Z, Zhang T, Chen H, Zhu W, Sartor RB, Boedeker EC, Harpaz N, Pace NR, Li E: Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases. Inflamm Bowel Dis. 2010, 17: 179-184.

Peterson DA, Frank DN, Pace NR, Gordon JI: Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases. Cell Host Microbe. 2008, 3: 417-427. 10.1016/j.chom.2008.05.001.

Nagalingam NA, Kao JY, Young VB: Microbial ecology of the murine gut associated with the development of dextran sodium sulfate-induced colitis. Inflamm Bowel Dis. 2011, 17: 917-26. 10.1002/ibd.21462.

Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI: An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006, 444: 1027-1031. 10.1038/nature05414.

Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI: A core gut microbiome in obese and lean twins. Nature. 2009, 457: 480-484. 10.1038/nature07540.

Zhang H, DiBaise JK, Zuccolo A, Kudrna D, Braidotti M, Yu Y, Parameswaran P, Crowell MD, Wing R, Rittmann BE, Krajmalnik-Brown R: Human gut microbiota in obesity and after gastric bypass. Proc Natl Acad Sci USA. 2009, 106: 2365-2370. 10.1073/pnas.0812600106.

Wu H-J, Ivanov II, Darce J, Hattori K, Shima T, Umesaki Y, Littman DR, Benoist C, Mathis D: Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells. Immunity. 2010, 32: 815-827. 10.1016/j.immuni.2010.06.001.

Ochoa-Repáraz J, Mielcarz DW, Ditrio LE, Burroughs AR, Foureau DM, Haque-Begum S, Kasper LH: Role of gut commensal microflora in the development of experimental autoimmune encephalomyelitis. J Immunol. 2009, 183: 6041-6050. 10.4049/jimmunol.0900747.

Yokote H, Miyake S, Croxford JL, Oki S, Mizusawa H, Yamamura T: NKT cell-dependent amelioration of a mouse model of multiple sclerosis by altering gut flora. Am J Pathol. 2008, 173: 1714-1723. 10.2353/ajpath.2008.080622.

Giongo A, Gano KA, Crabb DB, Mukherjee N, Novelo LL, Casella G, Drew JC, Ilonen J, Knip M, Hyöty H, Veijola R, Simell T, Simell O, Neu J, Wasserfall CH, Schatz D, Atkinson MA, Triplett EW: Toward defining the autoimmune microbiome for type 1 diabetes. ISME J. 2011, 5: 82-91. 10.1038/ismej.2010.92.

Brown CT, Davis-Richardson AG, Giongo A, Gano KA, Crabb DB, Mukherjee N, Casella G, Drew JC, Ilonen J, Knip M, Hyöty H, Veijola R, Simell T, Simell O, Neu J, Wasserfall CH, Schatz D, Atkinson MA, Triplett EW: Gut microbiome metagenomics analysis suggests a functional model for the development of autoimmunity for type 1 diabetes. PloS One. 2011, 6: e25792-10.1371/journal.pone.0025792.

Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D, Peng Y, Zhang D, Jie Z, Wu W, Qin Y, Xue W, Li J, Han L, Lu D, Wu P, Dai Y, Sun X, Li Z, Tang A, Zhong S, Li X, Chen W, Xu R, Wang M, Feng Q, et al: A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012, 490: 55-60. 10.1038/nature11450.

Russell SL, Gold MJ, Hartmann M, Willing BP, Thorson L, Wlodarska M, Gill N, Blanchet M-R, Mohn WW, McNagny KM, Finlay BB: Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma. EMBO Rep. 2012, 13: 440-447. 10.1038/embor.2012.32.

Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto J-M, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, et al: A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010, 464: 59-65. 10.1038/nature08821.

Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto J-M, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, et al: Enterotypes of the human gut microbiome. Nature. 2011, 473: 174-180. 10.1038/nature09944.

Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, Takami H, Morita H, Sharma VK, Srivastava TP, Taylor TD, Noguchi H, Mori H, Ogura Y, Ehrlich DS, Itoh K, Takagi T, Sakaki Y, Hayashi T, Hattori M: Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 2007, 14: 169-181. 10.1093/dnares/dsm018.

Curtis H, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT, Creasy HH, Earl AM, FitzGerald MG, Fulton RS, Giglio MG, Hallsworth-Pepin K, Lobos EA, Madupu R, Magrini V, Martin JC, Mitreva M: Structure, function and diversity of the human microbiome in an adult reference population. Nature. 2012, 486: 207-214. 10.1038/nature11234.

Zoetendal EG, Von Wright A, Vilpponen-Salmela T, Ben-Amor K, Akkermans ADL, De Vos WM: Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Appl Environ Microbiol. 2002, 68: 3401-3407. 10.1128/AEM.68.7.3401-3407.2002.

Booijink CCGM, El-Aidy S, Rajilić-Stojanović M, Heilig HGHJ, Troost FJ, Smidt H, Kleerebezem M, De Vos WM, Zoetendal EG: High temporal and inter-individual variation detected in the human ileal microbiota. Environ Microbiol. 2010, 12: 3213-3227. 10.1111/j.1462-2920.2010.02294.x.

Aguirre de Cárcer D, Cuív PO, Wang T, Kang S, Worthley D, Whitehall V, Gordon I, McSweeney C, Leggett B, Morrison M: Numerical ecology validates a biogeographical distribution and gender-based effect on mucosa-associated bacteria along the human colon. ISME J. 2011, 5: 801-809. 10.1038/ismej.2010.177.

Dethlefsen L, Relman DA: Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci USA. 2011, 108 (Suppl): 4554-4561. 10.1073/pnas.1000087107.

Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R: Bacterial community variation in human body habitats across space and time. Science. 2009, 326: 1694-1697. 10.1126/science.1177486.

Hildebrandt MA, Hoffmann C, Sherrill-Mix SA, Keilbaugh SA, Hamady M, Chen YY, Knight R, Ahima RS, Bushman F, Wu GD: High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology. 2009, 137: 1712-1716.

Tilg H: Obesity, metabolic syndrome, and microbiota: multiple interactions. J Clin Gastroenterol. 2010, 44 (Suppl 1): S16-18.

Wu GD, Chen J, Hoffmann C, Bittinger K, Chen Y-Y, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD: Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011, 334: 105-108. 10.1126/science.1208344.

Antunes LCM, Finlay BB: A comparative analysis of the effect of antibiotic treatment and enteric infection on intestinal homeostasis. Gut Microbes. 2011, 2: 105-108. 10.4161/gmic.2.2.15610.

Biasucci G, Rubini M, Riboni S, Morelli L, Bessi E, Retetangos C: Mode of delivery affects the bacterial community in the newborn gut. Early Hum Dev. 2010, 86: 13-15.

Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R: Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci USA. 2010, 107: 11971-11975. 10.1073/pnas.1002601107.

Adlerberth I: Factors influencing the establishment of the intestinal microbiota in infancy. Nestle Nutr Workshop Ser Pediatr Program. 2008, 62: 13-29. discussion 29-33

Falk PG, Hooper LV, Midtvedt T, Gordon JI: Creating and maintaining the gastrointestinal ecosystem: what we know and need to know from gnotobiology. Microbiol Mol Biol Rev. 1998, 62: 1157-1170.

Macpherson AJ, Harris NL: Interactions between commensal intestinal bacteria and the immune system. Nat Rev Immunol. 2004, 4: 478-485. 10.1038/nri1373.

Wen L, Ley RE, Volchkov PY, Stranges PB, Avanesyan L, Stonebraker AC, Hu C, Wong FS, Szot GL, Bluestone JA, Gordon JI, Chervonsky AV: Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature. 2008, 455: 1109-1113. 10.1038/nature07336.

Faith JJ, McNulty NP, Rey FE, Gordon JI: Predicting a human gut microbiota's response to diet in gnotobiotic mice. Science. 2011, 333: 101-104. 10.1126/science.1206025.

Faith JJ, Rey FE, O'Donnell D, Karlsson M, McNulty NP, Kallstrom G, Goodman AL, Gordon JI: Creating and characterizing communities of human gut microbes in gnotobiotic mice. ISME J. 2010, 4: 1094-1098. 10.1038/ismej.2010.110.

Goodman AL, Kallstrom G, Faith JJ, Reyes A, Moore A, Dantas G, Gordon JI: Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc Natl Acad Sci USA. 2011, 108: 6252-6257. 10.1073/pnas.1102938108.

Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI: The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med. 2009, 1: 6ra14-10.1126/scitranslmed.3000322.

Albert EJ, Sommerfeld K, Gophna S, Marshall JS, Gophna U: The gut microbiota of toll-like receptor 2-deficient mice exhibits lineage-specific modifications. Environ Microbiol Rep. 2009, 1: 65-70. 10.1111/j.1758-2229.2008.00006.x.

Xue X, Feng T, Yao S, Wolf KJ, Liu C-G, Liu X, Elson CO, Cong Y: Microbiota downregulates dendritic cell expression of miR-10a, which targets IL-12/IL-23p40. J Immunol. 2011, 187: 5879-5886. 10.4049/jimmunol.1100535.

Mondot S, Barreau F, Al Nabhani Z, Dussaillant M, Le Roux K, Doré J, Leclerc M, Hugot J-P, Lepage P: Altered gut microbiota composition in immune-impaired Nod2(-/-) mice. Gut. 2012, 61: 634-635. 10.1136/gutjnl-2011-300478.

Brinkman BM, Hildebrand F, Kubica M, Goosens D, Del Favero J, Declercq W, Raes J, Vandenabeele P: Caspase deficiency alters the murine gut microbiome. Cell Death Dis. 2011, 2: e220-10.1038/cddis.2011.101.

Bruno MEC, Rogier EW, Frantz AL, Stefka AT, Thompson SN, Kaetzel CS: Regulation of the polymeric immunoglobulin receptor in intestinal epithelial cells by Enterobacteriaceae: implications for mucosal homeostasis. Immunol Invest. 2010, 39: 356-382. 10.3109/08820131003622809.

Wells JM, Rossi O, Meijerink M, Van Baarlen P: Epithelial crosstalk at the microbiota-mucosal interface. Proc Natl Acad Sci USA. 2011, 108 (Suppl): 4607-4614. 10.1073/pnas.1000092107.

Wang Y, Devkota S, Musch MW, Jabri B, Nagler C, Antonopoulos DA, Chervonsky A, Chang EB: Regional mucosa-associated microbiota determine physiological expression of TLR2 and TLR4 in murine colon. PloS One. 2010, 5: e13607-10.1371/journal.pone.0013607.

Kellermayer R, Dowd SE, Harris RA, Balasa A, Schaible TD, Wolcott RD, Tatevian N, Szigeti R, Li Z, Versalovic J, Smith CW: Colonic mucosal DNA methylation, immune response, and microbiome patterns in Toll-like receptor 2-knockout mice. FASEB J. 2011, 25: 1449-1460. 10.1096/fj.10-172205.

Zhang C, Zhang M, Wang S, Han R, Cao Y, Hua W, Mao Y, Zhang X, Pang X, Wei C, Zhao G, Chen Y, Zhao L: Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice. ISME J. 2010, 4: 232-241. 10.1038/ismej.2009.112.

Deloris Alexander A, Orcutt RP, Henry JC, Baker J, Bissahoyo AC, Threadgill DW: Quantitative PCR assays for mouse enteric flora reveal strain-dependent differences in composition that are influenced by the microenvironment. Mamm Genome. 2006, 17: 1093-1104. 10.1007/s00335-006-0063-1.

Elinav E, Strowig T, Kau AL, Henao-Mejia J, Thaiss CA, Booth CJ, Peaper DR, Bertin J, Eisenbarth SC, Gordon JI, Flavell RA: NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell. 2011, 145: 745-757. 10.1016/j.cell.2011.04.022.

Saric J, Wang Y, Li J, Coen M, Utzinger J, Marchesi JR, Keiser J, Veselkov K, Lindon JC, Nicholson JK, Holmes E: Species variation in the fecal metabolome gives insight into differential gastrointestinal function. J Proteome Res. 2008, 7: 352-360. 10.1021/pr070340k.

Friswell MK, Gika H, Stratford IJ, Theodoridis G, Telfer B, Wilson ID, McBain AJ: Site and strain-specific variation in gut microbiota profiles and metabolism in experimental mice. PloS One. 2010, 5: e8584-10.1371/journal.pone.0008584.

Kovacs A, Ben-Jacob N, Tayem H, Halperin E, Iraqi F, Gophna U: Genotype is a stronger determinant than sex of the mouse gut microbiota. Microbial Ecol. 2011, 61: 423-428. 10.1007/s00248-010-9787-2.

Benson AK, Kelly S, Legge R, Ma F, Low SJ, Kim J, Zhang M, Oh PL, Nehrenberg D, Hua K, Kachman SD, Moriyama EN, Walter J, Peterson D, Pomp D: Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc Natl Acad Sci USA. 2010, 107: 18933-18938. 10.1073/pnas.1007028107.

Grönlund M-M, Grześkowiak Ł, Isolauri E, Salminen S: Influence of mother's intestinal microbiota on gut colonization in the infant. Gut microbes. 2011, 2: 227-233. 10.4161/gmic.2.4.16799.

Liu Z, Lozupone C, Hamady M, Bushman FD, Knight R: Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res. 2007, 35: e120-10.1093/nar/gkm541.

Liu Z, DeSantis TZ, Andersen GL, Knight R: Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res. 2008, 36: e120-10.1093/nar/gkn491.

Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methé B, DeSantis TZ, Petrosino JF, Knight R, Birren BW: Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 2011, 21: 494-504. 10.1101/gr.112730.110.

Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI: Obesity alters gut microbial ecology. Proc Natl Acad Sci USA. 2005, 102: 11070-11075. 10.1073/pnas.0504978102.

Kaufman L, Rousseeuw PJ: Finding Groups in Data: An Introduction to Cluster Analysis. 1990, Wiley-Interscience

Zupancic ML, Cantarel BL, Liu Z, Drabek EF, Ryan K, Cirimotich S, Jones C, Knight R, Walters W, Knights D, Mongodin EF, Horenstein RB, Mitchell BD, Steinle N, Snitker S, Shuldiner AR, Fraser CM: Analysis of the gut microbiota in the Old Order Amish and its relation to the metabolic syndrome. PLoS ONE. 2012, 7: e43052-10.1371/journal.pone.0043052.

D'Haens G, Ferrante M, Vermeire S, Baert F, Noman M, Moortgat L, Geens P, Iwens D, Aerden I, Van Assche G, Van Olmen G, Rutgeerts P: Fecal calprotectin is a surrogate marker for endoscopic lesions in inflammatory bowel disease. Inflamm Bowel Dis. 2012, 18: 2218-2224. 10.1002/ibd.22917.

Shulman RJ, Eakin MN, Czyzewski DI, Jarrett M, Ou C-N: Increased gastrointestinal permeability and gut inflammation in children with functional abdominal pain and irritable bowel syndrome. J Pediatr. 2008, 153: 646-650. 10.1016/j.jpeds.2008.04.062.

Yang H, Wang JR, Didion JP, Buus RJ, Bell TA, Welsh CE, Bonhomme F, Yu AH-T, Nachman MW, Pialek J, Tucker P, Boursot P, McMillan L, Churchill GA, De Villena FP-M: Subspecific origin and haplotype diversity in the laboratory mouse. Nat Genet. 2011, 43: 648-655. 10.1038/ng.847.

Van Passel MWJ, Kant R, Zoetendal EG, Plugge CM, Derrien M, Malfatti SA, Chain PSG, Woyke T, Palva A, De Vos WM, Smidt H: The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes. PloS One. 2011, 6: e16876-10.1371/journal.pone.0016876.

Taylor NS, Xu S, Nambiar P, Dewhirst FE, Fox JG: Enterohepatic Helicobacter species are prevalent in mice from commercial and academic institutions in Asia, Europe, and North America. J Clin Microbiol. 2007, 45: 2166-2172. 10.1128/JCM.00137-07.

Rehman A, Lepage P, Nolte A, Hellmig S, Schreiber S, Ott SJ: Transcriptional activity of the dominant gut mucosal microbiota in chronic inflammatory bowel disease patients. J Med Microbiol. 2010, 59: 1114-1122. 10.1099/jmm.0.021170-0.

Willing BP, Dicksved J, Halfvarson J, Andersson AF, Lucio M, Zheng Z, Järnerot G, Tysk C, Jansson JK, Engstrand L: A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology. 2010, 139: 1844-1854. 10.1053/j.gastro.2010.08.049. e1

Maes M, Mihaylova I, Leunis J-C: Increased serum IgA and IgM against LPS of enterobacteria in chronic fatigue syndrome (CFS): indication for the involvement of gram-negative enterobacteria in the etiology of CFS and for the presence of an increased gut-intestinal permeability. J Affect Disord. 2007, 99: 237-240. 10.1016/j.jad.2006.08.021.

Arthur JC, Perez-Chanona E, Mühlbauer M, Tomkovich S, Uronis JM, Fan T-J, Campbell BJ, Abujamel T, Dogan B, Rogers AB, Rhodes JM, Stintzi A, Simpson KW, Hansen JJ, Keku TO, Fodor AA, Jobin C: Intestinal inflammation targets cancer-inducing activity of the microbiota. Science. 2012, 117: 1175-1183.

Lozupone C, Stombaugh JI, Gordon JI, Jansson JK, Knight R: Diversity, stability and resilience of the human gut microbiota. Nature. 2012, 489: 220-230. 10.1038/nature11550.

Fernandez-Raudales D, Hoeflinger J, Bringe NA, Cox SB, Dowd SE, Miller MJ, Gonzalez de Mejia E: Consumption of different soymilk formulations differentially affects the gut microbiomes of overweight and obese men. Gut Microbes. 2012, 3: 490-500. 10.4161/gmic.21578.

Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone C, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI: Human gut microbiome viewed across age and geography. Nature. 2012, 486: 222-227.

Neyrinck AM, Possemiers S, Druart C, Van de Wiele T, De Backer F, Cani PD, Larondelle Y, Delzenne NM: Prebiotic effects of wheat arabinoxylan related to the increase in bifidobacteria, Roseburia and Bacteroides/Prevotella in diet-induced obese mice. PloS One. 2011, 6: e20944-10.1371/journal.pone.0020944.

Salzman NH, Hung K, Haribhai D, Chu H, Karlsson-Sjöberg J, Amir E, Teggatz P, Barman M, Hayward M, Eastwood D, Stoel M, Zhou Y, Sodergren E, Weinstock GM, Bevins CL, Williams CB, Bos N: Enteric defensins are essential regulators of intestinal microbial ecology. Nat Immunol. 2010, 11: 76-83. 10.1038/ni.1825.

Shanahan MT, Tanabe H, Ouellette AJ: Strain-specific polymorphisms in Paneth cell α-defensins of C57BL/6 mice and evidence of vestigial myeloid α-defensin pseudogenes. Infect Immun. 2011, 79: 459-473. 10.1128/IAI.00996-10.

Islam KBMS, Fukiya S, Hagio M, Fujii N, Ishizuka S, Ooka T, Ogura Y, Hayashi T, Yokota A: Bile acid is a host factor that regulates the composition of the cecal microbiota in rats. Gastroenterology. 2011, 141: 1773-1781. 10.1053/j.gastro.2011.07.046.

Wang DQ, Paigen B, Carey MC: Genetic factors at the enterocyte level account for variations in intestinal cholesterol absorption efficiency among inbred strains of mice. J Lipid Res. 2001, 42: 1820-1830.

Wang DQ-H, Lammert F, Paigen B, Carey MC: Phenotypic characterization of Lith genes that determine susceptibility to cholesterol cholelithiasis in inbred mice: pathophysiology of biliary lipid secretion. J Lipid Res. 1999, 40: 2066-2079.

Stecher B, Chaffron S, Käppeli R, Hapfelmeier S, Freedrich S, Weber TC, Kirundi J, Suar M, McCoy KD, Von Mering C, Macpherson AJ, Hardt W-D: Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathog. 2010, 6: e1000711-10.1371/journal.ppat.1000711.

Zoetendal EG, Heilig HG, Klaassens ES, Booijink CC, Kleerebezem M, Smidt H, De Vos WM: Isolation of DNA from bacterial samples of the human gastrointestinal tract. Nat Protoc. 2006, 1: 870-873. 10.1038/nprot.2006.142.

Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R: QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010, 7: 335-336. 10.1038/nmeth.f.303.

Edgar RC: Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010, 26: 2460-2461. 10.1093/bioinformatics/btq461.

Wang Q, Garrity GM, Tiedje JM, Cole JR: Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007, 73: 5261-5267. 10.1128/AEM.00062-07.

Endres D, Schindelin J: A new metric for probability distributions. IEEE Trans Information Theory. 2003, 49: 1858-1860. 10.1109/TIT.2003.813506.

Bray JR, Curtis JT: An ordination of the upland forest communities of Southern Wisconsin. Ecol Monographs. 1957, 27: 325-10.2307/1942268.

Lozupone C, Hamady M, Knight R: UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics. 2006, 7: 371-10.1186/1471-2105-7-371.

Anderson M: A new method for non-parametric multivariate analysis of variance. Austral Ecol. 2001, 32-46.

Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B. 1995, 289-300.

Borcard D, Legendre P, Drapeau P: Partialling out the spatial component of ecological variation. Ecology. 1992, 73: 1045-10.2307/1940179.

Anderson MJ: Distance-based tests for homogeneity of multivariate dispersions. Biometrics. 2006, 62: 245-253. 10.1111/j.1541-0420.2005.00440.x.

Hothorn T, Hornik K, Van de Wiel MA, Zeileis A: A Lego system for conditional inference. Am Stat. 2006, 60: 257-263. 10.1198/000313006X118430.

Chao A: Nonparametric-estimation of the number of classes in a population. Scand J Stat. 1984, 11: 265-270.

Shannon CE: A mathematical theory of communication. Bell System Tech J. 1948, 27: 379-423.

Mantel N: The detection of disease clustering and a generalized regression approach. Cancer Res. 1967, 27: 209-220.

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Genome Biology

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