β2→1-Fructans Modulate the Immune System In Vivo in a Microbiota-Dependent and -Independent Fashion

Mowat, 2014, Regional specialization within the intestinal immune system, Nat Rev Immunol, 14, 667, 10.1038/nri3738

Cho, 2012, The human microbiome: at the interface of health and disease, Nat Rev Genet, 13, 260, 10.1038/nrg3182

Klaenhammer, 2012, The impact of probiotics and prebiotics on the immune system, Nat Rev Immunol, 12, 728, 10.1038/nri3312

Roberfroid, 2007, Inulin-type fructans: functional food ingredients, J Nutr, 137, 2493S, 10.1093/jn/137.11.2493S

Gibson, 2004, Dietary modulation of the human colonic microbiota: updating the concept of prebiotics, Nutr Res Rev, 17, 259, 10.1079/NRR200479

Vogt, 2015, Immunological properties of inulin-type fructans, Crit Rev Food Sci Nutr, 55, 414, 10.1080/10408398.2012.656772

Nakamura, 2004, Dietary fructooligosaccharides up-regulate immunoglobulin A response and polymeric immunoglobulin receptor expression in intestines of infant mice, Clin Exp Immunol, 137, 52, 10.1111/j.1365-2249.2004.02487.x

Hosono, 2003, Dietary fructooligosaccharides induce immunoregulation of intestinal IgA secretion by murine Peyer’s patch cells, Biosci Biotechnol Biochem, 67, 758, 10.1271/bbb.67.758

Ryz, 2009, Long-chain inulin increases dendritic cells in the Peyer’s patches and increases ex vivo cytokine secretion in the spleen and mesenteric lymph nodes of growing female rats, independent of zinc status, Br J Nutr, 101, 1653, 10.1017/S000711450812342X

Roberfroid, 2010, Prebiotic effects: metabolic and health benefits, Br J Nutr, 104, S1, 10.1017/S0007114510003363

Julia, 2015, The impact of diet on asthma and allergic diseases, Nat Rev Immunol, 15, 308, 10.1038/nri3830

Meijer, 2010, Butyrate and other short-chain fatty acids as modulators of immunity: what relevance for health?, Curr Opin Clin Nutr Metab Care, 13, 715, 10.1097/MCO.0b013e32833eebe5

Macia, 2015, Metabolite-sensing receptors GPR43 and GPR109A facilitate dietary fibre-induced gut homeostasis through regulation of the inflammasome, Nat Commun, 6, 6734, 10.1038/ncomms7734

Smith, 2013, The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis, Science, 341, 569, 10.1126/science.1241165

Vogt, 2013, Immune modulation by different types of β2→1-fructans is toll-like receptor dependent, PLoS One, 8, e68367, 10.1371/journal.pone.0068367

Sonnenburg, 2014, Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates, Cell Metab, 20, 779, 10.1016/j.cmet.2014.07.003

Gentleman, 2004, Bioconductor: open software development for computational biology and bioinformatics, Genome Biol, 5, R80, 10.1186/gb-2004-5-10-r80

Lin, 2011, MADMAX – management and analysis database for multiple ~omics experiments, J Integr Bioinform, 8, 160, 10.2390/biecoll-jib-2011-160

Dai, 2005, Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data, Nucleic Acids Res, 33, e175, 10.1093/nar/gni179

Bolstad, 2004, Experimental design and low-level analysis of microarray data, Int Rev Neurobiol, 60, 25, 10.1016/S0074-7742(04)60002-X

Berry, 2011, Barcoded primers used in multiplex amplicon pyrosequencing bias amplification, Appl Environ Microbiol, 77, 7846, 10.1128/AEM.05220-11

Yu, 2004, Improved extraction of PCR-quality community DNA from digesta and fecal samples, Biotechniques, 36, 808, 10.2144/04365ST04

Van den Bogert, 2013, Diversity of human small intestinal Streptococcus and Veillonella populations, FEMS Microbiol Ecol, 85, 376, 10.1111/1574-6941.12127

Van den Bogert, 2011, Microarray analysis and barcoded pyrosequencing provide consistent microbial profiles depending on the source of human intestinal samples, Appl Environ Microbiol, 77, 2071, 10.1128/AEM.02477-10

Quast, 2013, The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Res, 41, D590, 10.1093/nar/gks1219

Caporaso, 2010, QIIME allows analysis of high-throughput community sequencing data, Nat Methods, 7, 335, 10.1038/nmeth.f.303

Storey, 2003, Statistical significance for genomewide studies, Proc Natl Acad Sci U S A, 100, 9440, 10.1073/pnas.1530509100

Sartor, 2006, Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments, BMC Bioinformatics, 7, 538, 10.1186/1471-2105-7-538

Ainsworth, 2015, The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts, ISME J, 9, 2261, 10.1038/ismej.2015.39

Goto, 2014, Innate lymphoid cells regulate intestinal epithelial cell glycosylation, Science, 345, 1254009, 10.1126/science.1254009

Pham, 2014, Epithelial IL-22RA1-mediated fucosylation promotes intestinal colonization resistance to an opportunistic pathogen, Cell Host Microbe, 16, 504, 10.1016/j.chom.2014.08.017

Ivanov, 2009, Induction of intestinal Th17 cells by segmented filamentous bacteria, Cell, 139, 485, 10.1016/j.cell.2009.09.033

Vieira, 2013, The role of probiotics and prebiotics in inducing gut immunity, Front Immunol, 4, 445, 10.3389/fimmu.2013.00445

Kim, 2014, Gut microbiota-derived short-chain fatty acids, T cells, and inflammation, Immune Netw, 14, 277, 10.4110/in.2014.14.6.277

Ito, 2011, Degree of polymerization of inulin-type fructans differentially affects number of lactic acid bacteria, intestinal immune functions, and immunoglobulin A secretion in the rat cecum, J Agric Food Chem, 59, 5771, 10.1021/jf200859z

Ito, 2008, The degree of polymerization of inulin-like fructans affects cecal mucin and immunoglobulin A in rats, J Food Sci, 73, H36, 10.1111/j.1750-3841.2008.00686.x

Aidy, 2015, The small intestine microbiota, nutritional modulation and relevance for health, Curr Opin Biotechnol, 32, 14, 10.1016/j.copbio.2014.09.005

Pasare, 2005, Control of B-cell responses by toll-like receptors, Nature, 438, 364, 10.1038/nature04267

Pickard, 2014, Rapid fucosylation of intestinal epithelium sustains host-commensal symbiosis in sickness, Nature, 514, 638, 10.1038/nature13823

Hooper, 1999, A molecular sensor that allows a gut commensal to control its nutrient foundation in a competitive ecosystem, Proc Natl Acad Sci U S A, 96, 9833, 10.1073/pnas.96.17.9833

Coyne, 2005, Human symbionts use a host-like pathway for surface fucosylation, Science, 307, 1778, 10.1126/science.1106469

Koda, 2001, Contrasting patterns of polymorphisms at the ABO-secretor gene (FUT2) and plasma {{alpha}}(1,3)fucosyltransferase gene (FUT6) in human populations, Genetics, 158, 747, 10.1093/genetics/158.2.747

Wacklin, 2011, Secretor genotype (FUT2 gene) is strongly associated with the composition of Bifidobacteria in the human intestine, PLoS One, 6, e20113, 10.1371/journal.pone.0020113

Kambhampati, 2016, Host genetic susceptibility to enteric viruses: a systematic review and metaanalysis, Clin Infect Dis, 62, 11, 10.1093/cid/civ873

McGovern, 2010, Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn’s disease, Hum Mol Genet, 19, 3468, 10.1093/hmg/ddq248