Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207–14.
Article
Google Scholar
Human Microbiome Project Consortium. A framework for human microbiome research. Nature. 2012;486:215–21.
Article
Google Scholar
Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, et al. An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol. 2014;32:834–41.
Article
CAS
PubMed
Google Scholar
Sommer F, Backhed F. The gut microbiota - masters of host development and physiology. Nat Rev Microbiol. 2013;11:227–38.
Article
CAS
PubMed
Google Scholar
Karlsson FH, Fåk F, Nookaew I, Tremaroli V, Fagerberg B, Petranovic D, et al. Symptomatic atherosclerosis is associated with an altered gut metagenome. Nat Commun. 2012;3:1245.
Article
PubMed Central
PubMed
Google Scholar
Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature. 2006;444:1022–3.
Article
CAS
PubMed
Google Scholar
Ott SJ, Musfeldt M, Wenderoth DF, Hampe J, Brant O, Folsch UR, et al. Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut. 2004;53:685–93.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sekirov I, Russell SL, Antunes LC, Finlay BB. Gut microbiota in health and disease. Physiol Rev. 2010;90:859–904.
Article
CAS
PubMed
Google Scholar
Kleerebezem M, Vaughan EE. Probiotic and gut lactobacilli and bifidobacteria: molecular approaches to study diversity and activity. Annu Rev Microbiol. 2009;63:269–90.
Article
CAS
PubMed
Google Scholar
Medema JP, Vermeulen L. Microenvironmental regulation of stem cells in intestinal homeostasis and cancer. Nature. 2011;474:318–26.
Article
CAS
PubMed
Google Scholar
El Aidy S, Derrien M, Merrifield CA, Levenez F, Dore J, Boekschoten MV, et al. Gut bacteria-host metabolic interplay during conventionalisation of the mouse germfree colon. ISME J. 2013;7:743–55.
Article
PubMed Central
PubMed
Google Scholar
Gaboriau-Routhiau V, Rakotobe S, Lecuyer E, Mulder I, Lan A, Bridonneau C, et al. The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity. 2009;31:677–89.
Article
CAS
PubMed
Google Scholar
El Aidy S, Merrifield CA, Derrien M, van Baarlen P, Hooiveld G, Levenez F, et al. The gut microbiota elicits a profound metabolic reorientation in the mouse jejunal mucosa during conventionalisation. Gut. 2013;62:1306–14.
Article
PubMed
Google Scholar
El Aidy S, van Baarlen P, Derrien M, Lindenbergh-Kortleve DJ, Hooiveld G, Levenez F, et al. Temporal and spatial interplay of microbiota and intestinal mucosa drive establishment of immune homeostasis in conventionalized mice. Mucosal Immunol. 2012;5:567–79.
PubMed
Google Scholar
Larsson E, Tremaroli V, Lee YS, Koren O, Nookaew I, Fricker A, et al. Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88. Gut. 2012;61:1124–31.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kijani S, Yrlid U, Heyden M, Levin M, Boren J, Fogelstrand P. Filter-dense multicolor microscopy. PLoS One. 2015;10, e0119499.
Article
PubMed Central
PubMed
Google Scholar
Abrams GD, Bauer H, Sprinz H. Influence of the normal flora on mucosal morphology and cellular renewal in the ileum. A comparison of germ-free and conventional mice. Lab Invest. 1963;12:355–64.
CAS
PubMed
Google Scholar
den Hollander J, Rimpi S, Doherty JR, Rudelius M, Buck A, Hoellein A, et al. Aurora kinases A and B are up-regulated by Myc and are essential for maintenance of the malignant state. Blood. 2010;116:1498–505.
Article
Google Scholar
Haugwitz U, Wasner M, Wiedmann M, Spiesbach K, Rother K, Mossner J, et al. A single cell cycle genes homology region (CHR) controls cell cycle-dependent transcription of the cdc25C phosphatase gene and is able to cooperate with E2F or Sp1/3 sites. Nucleic Acids Res. 2002;30:1967–76.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ngo CV, Gee M, Akhtar N, Yu D, Volpert O, Auerbach R, et al. An in vivo function for the transforming Myc protein: elicitation of the angiogenic phenotype. Cell Growth Differ. 2000;11:201–10.
PubMed Central
CAS
PubMed
Google Scholar
Rogoff HA, Pickering MT, Frame FM, Debatis ME, Sanchez Y, Jones S, et al. Apoptosis associated with deregulated E2F activity is dependent on E2F1 and Atm/Nbs1/Chk2. Mol Cell Biol. 2004;24:2968–77.
Article
PubMed Central
CAS
PubMed
Google Scholar
Stanelle J, Stiewe T, Theseling CC, Peter M, Putzer BM. Gene expression changes in response to E2F1 activation. Nucleic Acids Res. 2002;30:1859–67.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yan Z, DeGregori J, Shohet R, Leone G, Stillman B, Nevins JR, et al. Cdc6 is regulated by E2F and is essential for DNA replication in mammalian cells. Proc Natl Acad Sci U S A. 1998;95:3603–8.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zeller KI, Zhao X, Lee CW, Chiu KP, Yao F, Yustein JT, et al. Global mapping of c-Myc binding sites and target gene networks in human B cells. Proc Natl Acad Sci U S A. 2006;103:17834–9.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bruno ME, Frantz AL, Rogier EW, Johansen FE, Kaetzel CS. Regulation of the polymeric immunoglobulin receptor by the classical and alternative NF-kappaB pathways in intestinal epithelial cells. Mucosal Immunol. 2011;4:468–78.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chen L, Yang G, Zhang X, Wu J, Gu Q, Wei M, et al. Induction of MIF expression by oxidized LDL via activation of NF-kappaB in vascular smooth muscle cells. Atherosclerosis. 2009;207:428–33.
Article
CAS
PubMed
Google Scholar
Cho ML, Moon YM, Heo YJ, Woo YJ, Ju JH, Park KS, et al. NF-kappaB inhibition leads to increased synthesis and secretion of MIF in human CD4+ T cells. Immunol Lett. 2009;123:21–30.
Article
CAS
PubMed
Google Scholar
Dommels YE, Butts CA, Zhu S, Davy M, Martell S, Hedderley D, et al. Characterization of intestinal inflammation and identification of related gene expression changes in mdr1a(−/−) mice. Genes Nutr. 2007;2:209–23.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ruffell D, Mourkioti F, Gambardella A, Kirstetter P, Lopez RG, Rosenthal N, et al. A CREB-C/EBPbeta cascade induces M2 macrophage-specific gene expression and promotes muscle injury repair. Proc Natl Acad Sci U S A. 2009;106:17475–80.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sommer F, Backhed F. The gut microbiota engages different signaling pathways to induce Duox2 expression in the ileum and colon epithelium. Mucosal Immunol. 2015;8:372–9.
Article
CAS
PubMed
Google Scholar
Takenouchi-Ohkubo N, Takahashi T, Tsuchiya M, Mestecky J, Moldoveanu Z, Moro I. Role of nuclear factor-kappaB in the expression by tumor necrosis factor-alpha of the human polymeric immunoglobulin receptor (plgR) gene. Immunogenetics. 2000;51:289–95.
Article
CAS
PubMed
Google Scholar
Consortium EP. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57–74.
Article
Google Scholar
Obach M, Navarro-Sabate A, Caro J, Kong X, Duran J, Gomez M, et al. 6-Phosphofructo-2-kinase (pfkfb3) gene promoter contains hypoxia-inducible factor-1 binding sites necessary for transactivation in response to hypoxia. J Biol Chem. 2004;279:53562–70.
Article
CAS
PubMed
Google Scholar
Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res. 2012;22:1798–812.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wang ND, Finegold MJ, Bradley A, Ou CN, Abdelsayed SV, Wilde MD, et al. Impaired energy homeostasis in C/EBP alpha knockout mice. Science. 1995;269:1108–12.
Article
CAS
PubMed
Google Scholar
Whitfield TW, Wang J, Collins PJ, Partridge EC, Aldred SF, Trinklein ND, et al. Functional analysis of transcription factor binding sites in human promoters. Genome Biol. 2012;13:R50.
Article
PubMed Central
PubMed
Google Scholar
Encyclopedia of gut microbiota regulated genes. http://microbiota.wall.gu.se.
Donohoe DR, Garge N, Zhang X, Sun W, O’Connell TM, Bunger MK, et al. The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon. Cell Metab. 2011;13:517–26.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pott J, Stockinger S, Torow N, Smoczek A, Lindner C, McInerney G, et al. Age-dependent TLR3 expression of the intestinal epithelium contributes to rotavirus susceptibility. PLoS Pathog. 2012;8, e1002670.
Article
PubMed Central
CAS
PubMed
Google Scholar
Camp JG, Frank CL, Lickwar CR, Guturu H, Rube T, Wenger AM, et al. Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape. Genome Res. 2014;24:1504–16.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kim TH, Li F, Ferreiro-Neira I, Ho LL, Luyten A, Nalapareddy K, et al. Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity. Nature. 2014;506:511–5.
Article
PubMed Central
CAS
PubMed
Google Scholar
Geuking MB, Cahenzli J, Lawson MA, Ng DC, Slack E, Hapfelmeier S, et al. Intestinal bacterial colonization induces mutualistic regulatory T cell responses. Immunity. 2011;34:794–806.
Article
CAS
PubMed
Google Scholar
Bäckhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A. 2004;101:15718–23.
Article
PubMed Central
PubMed
Google Scholar
Sayin SI, Wahlstrom A, Felin J, Jantti S, Marschall HU, Bamberg K, et al. Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist. Cell Metab. 2013;17:225–35.
Article
CAS
PubMed
Google Scholar
Stappenbeck TS, Hooper LV, Gordon JI. Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. Proc Natl Acad Sci U S A. 2002;99:15451–5.
Article
PubMed Central
CAS
PubMed
Google Scholar
Alenghat T, Osborne LC, Saenz SA, Kobuley D, Ziegler CG, Mullican SE, et al. Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis. Nature. 2013;504:153–7.
Article
PubMed Central
CAS
PubMed
Google Scholar
Arpaia N, Campbell C, Fan X, Dikiy S, van der Veeken J, Deroos P, et al. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature. 2013;504:451–5.
Article
CAS
PubMed
Google Scholar
Kellermayer R, Dowd SE, Harris RA, Balasa A, Schaible TD, Wolcott RD, et al. Colonic mucosal DNA methylation, immune response, and microbiome patterns in Toll-like receptor 2-knockout mice. FASEB J. 2011;25:1449–60.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mischke M, Plosch T. More than just a gut instinct-the potential interplay between a baby’s nutrition, its gut microbiome, and the epigenome. Am J Physiol Regul Integr Comp Physiol. 2013;304:R1065–9.
Article
CAS
PubMed
Google Scholar
Leblond CP, Stevens CE. The constant renewal of the intestinal epithelium in the albino rat. Anat Rec. 1948;100:357–77.
Article
CAS
PubMed
Google Scholar
Creamer B, Shorter RG, Bamforth J. The turnover and shedding of epithelial cells I. The turnover in the gastro-intestinal tract. Gut. 1961;2:110–8.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hansson GC. Role of mucus layers in gut infection and inflammation. Curr Opin Microbiol. 2012;15:57–62.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sommer F, Adam N, Johansson MEV, Xia L, Hansson GC, Bäckhed F. Altered mucus glycosylation in core 1 O-glycan-deficient mice affects microbiota composition and intestinal architecture. PLoS One. 2014;9, e85254.
Article
PubMed Central
PubMed
Google Scholar
Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2004;3:1–25.
Google Scholar
Wilkerson MD, Hayes DN. ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics. 2010;26:1572–3.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zambelli F, Prazzoli GM, Pesole G, Pavesi G. Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets. Nucleic Acids Res. 2012;40:W510–5.
Article
PubMed Central
CAS
PubMed
Google Scholar
Loots G, Ovcharenko I. ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes. Bioinformatics. 2007;23:122–4.
Article
CAS
PubMed
Google Scholar
Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell. 2007;27:91–105.
Article
PubMed Central
CAS
PubMed
Google Scholar
Friedman RC, Farh KK, Burge CB, Bartel DP. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 2009;19:92–105.
Article
PubMed Central
CAS
PubMed
Google Scholar
John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Human MicroRNA targets. PLoS Biol. 2004;2, e363.
Article
PubMed Central
PubMed
Google Scholar
Betel D, Wilson M, Gabow A, Marks DS, Sander C. The microRNA.org resource: targets and expression. Nucleic Acids Res. 2008;36:D149–53.
Article
PubMed Central
CAS
PubMed
Google Scholar
Varemo L, Nielsen J, Nookaew I. Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods. Nucleic Acids Res. 2013;41:4378–91.
Article
PubMed Central
PubMed
Google Scholar