Gut microbiota influences low fermentable substrate diet efficacy in children with irritable bowel syndrome

References

• Rasquin A, Di Lorenzo C, Forbes D, Guiraldes E, Hyams JS, Staiano A, Walker LS. Childhood functional gastrointestinal disorders: child/adolescent. Gastroenterology 2006; 130:1527 - 37; http://dx.doi.org/10.1053/j.gastro.2005.08.063; PMID: 16678566
   PubMed Web of Science ®Google Scholar
• McOmber ME, Shulman RJ. Recurrent abdominal pain and irritable bowel syndrome in children. Curr Opin Pediatr 2007; 19:581 - 5; http://dx.doi.org/10.1097/MOP.0b013e3282bf6ddc; PMID: 17885479
   PubMed Web of Science ®Google Scholar
• Saulnier DM, Riehle K, Mistretta TA, Diaz MA, Mandal D, Raza S, Weidler EM, Qin X, Coarfa C, Milosavljevic A, et al. Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology 2011; 141:1782 - 91; http://dx.doi.org/10.1053/j.gastro.2011.06.072; PMID: 21741921
   PubMed Web of Science ®Google Scholar
• Austin GL, Dalton CB, Hu Y, Morris CB, Hankins J, Weinland SR, Westman EC, Yancy WS Jr., Drossman DA. A very low-carbohydrate diet improves symptoms and quality of life in diarrhea-predominant irritable bowel syndrome. Clin Gastroenterol Hepatol 2009; 7:706 - 8, e1; http://dx.doi.org/10.1016/j.cgh.2009.02.023; PMID: 19281859
   PubMed Web of Science ®Google Scholar
• Gibson PR, Shepherd SJ. Evidence-based dietary management of functional gastrointestinal symptoms: The FODMAP approach. J Gastroenterol Hepatol 2010; 25:252 - 8; http://dx.doi.org/10.1111/j.1440-1746.2009.06149.x; PMID: 20136989
   PubMed Web of Science ®Google Scholar
• Staudacher HM, Whelan K, Irving PM, Lomer MC. Comparison of symptom response following advice for a diet low in fermentable carbohydrates (FODMAPs) versus standard dietary advice in patients with irritable bowel syndrome. J Hum Nutr Diet 2011; 24:487 - 95; http://dx.doi.org/10.1111/j.1365-277X.2011.01162.x; PMID: 21615553
   PubMed Web of Science ®Google Scholar
• Ong DK, Mitchell SB, Barrett JS, Shepherd SJ, Irving PM, Biesiekierski JR, Smith S, Gibson PR, Muir JG. Manipulation of dietary short chain carbohydrates alters the pattern of gas production and genesis of symptoms in irritable bowel syndrome. J Gastroenterol Hepatol 2010; 25:1366 - 73; http://dx.doi.org/10.1111/j.1440-1746.2010.06370.x; PMID: 20659225
   PubMed Web of Science ®Google Scholar
• Staudacher HM, Lomer MC, Anderson JL, Barrett JS, Muir JG, Irving PM, Whelan K. Fermentable carbohydrate restriction reduces luminal bifidobacteria and gastrointestinal symptoms in patients with irritable bowel syndrome. J Nutr 2012; 142:1510 - 8; http://dx.doi.org/10.3945/jn.112.159285; PMID: 22739368
   PubMed Web of Science ®Google Scholar
• Gibson PR, Shepherd SJ. Food choice as a key management strategy for functional gastrointestinal symptoms. Am J Gastroenterol 2012; 107:657 - 66, quiz 667; http://dx.doi.org/10.1038/ajg.2012.49; PMID: 22488077
   PubMed Web of Science ®Google Scholar
• Shepherd SJ, Gibson PR. Fructose malabsorption and symptoms of irritable bowel syndrome: guidelines for effective dietary management. J Am Diet Assoc 2006; 106:1631 - 9; http://dx.doi.org/10.1016/j.jada.2006.07.010; PMID: 17000196
   PubMed Web of Science ®Google Scholar
• Grech-Mora IFM-L, Ollivier B, Rimbault A, Presnier G, Garcia J-L, Garnier-Sillam E. Isolation and characterization of Sporobacter termitidis gen. nov., sp. nov., from the digestive tract of the wood-feeding termite Nasutitermes lujae. Int J Syst Bacteriol 1996; 46:512 - 8; http://dx.doi.org/10.1099/00207713-46-2-512
   Google Scholar
• Del Dot TOR, Stackebrandt E. Phascolarctobacterium faecium gen. nov., sp. nov., a novel taxon of the Spormusa group of bacteria. Syst Appl Microbiol 1993; 16:380 - 4; http://dx.doi.org/10.1016/S0723-2020(11)80269-9
   Web of Science ®Google Scholar
• Flint HJ, Scott KP, Duncan SH, Louis P, Forano E. Microbial degradation of complex carbohydrates in the gut. Gut Microbes 2012; 3:289 - 306; http://dx.doi.org/10.4161/gmic.19897; PMID: 22572875
   PubMed Web of Science ®Google Scholar
• Tana C, Umesaki Y, Imaoka A, Handa T, Kanazawa M, Fukudo S. Altered profiles of intestinal microbiota and organic acids may be the origin of symptoms in irritable bowel syndrome. Neurogastroenterol Motil 2010; 22:512 - 9, e114-5; PMID: 19903265
   PubMed Web of Science ®Google Scholar
• Alles MS, Katan MB, Salemans JM, Van Laere KM, Gerichhausen MJ, Rozendaal MJ, Nagengast FM. Bacterial fermentation of fructooligosaccharides and resistant starch in patients with an ileal pouch-anal anastomosis. Am J Clin Nutr 1997; 66:1286 - 92; PMID: 9356550
   PubMed Web of Science ®Google Scholar
• Rasmussen HS, Holtug K, Mortensen PB. Degradation of amino acids to short-chain fatty acids in humans. An in vitro study. Scand J Gastroenterol 1988; 23:178 - 82; http://dx.doi.org/10.3109/00365528809103964; PMID: 3363290
   PubMed Web of Science ®Google Scholar
• Cotillard A, Kennedy SP, Kong LC, Prifti E, Pons N, Le Chatelier E, Almeida M, Quinquis B, Levenez F, Galleron N, et al, ANR MicroObes consortium. Dietary intervention impact on gut microbial gene richness. Nature 2013; 500:585 - 8; http://dx.doi.org/10.1038/nature12480; PMID: 23985875
   PubMed Web of Science ®Google Scholar
• Taras D, Simmering R, Collins MD, Lawson PA, Blaut M. Reclassification of Eubacterium formicigenerans Holdeman and Moore 1974 as Dorea formicigenerans gen. nov., comb. nov., and description of Dorea longicatena sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2002; 52:423 - 8; PMID: 11931151
   PubMed Web of Science ®Google Scholar
• Laube VM, Martin SM, SM LVaM. Conversion of cellulose to methane and carbon dioxide by triculture of Acetivibrio cellulolyticus, Desulfovibrio sp, and Methanosarcina barkeri. Appl Environ Microbiol 1981; 42:413 - 20; PMID: 16345841
   PubMed Web of Science ®Google Scholar
• Dear KL, Elia M, Hunter JO. Do interventions which reduce colonic bacterial fermentation improve symptoms of irritable bowel syndrome?. Dig Dis Sci 2005; 50:758 - 66; http://dx.doi.org/10.1007/s10620-005-2570-4; PMID: 15844715
   PubMed Web of Science ®Google Scholar
• Ong DK, Mitchell SB, Barrett JS, Shepherd SJ, Irving PM, Biesiekierski JR, Smith S, Gibson PR, Muir JG. Manipulation of dietary short chain carbohydrates alters the pattern of gas production and genesis of symptoms in irritable bowel syndrome. J Gastroenterol Hepatol 2010; 25:1366 - 73; http://dx.doi.org/10.1111/j.1440-1746.2010.06370.x; PMID: 20659225
   PubMed Web of Science ®Google Scholar
• Joossens M, Huys G, Cnockaert M, De Preter V, Verbeke K, Rutgeerts P, Vandamme P, Vermeire S. Dysbiosis of the faecal microbiota in patients with Crohn’s disease and their unaffected relatives. Gut 2011; 60:631 - 7; http://dx.doi.org/10.1136/gut.2010.223263; PMID: 21209126
   PubMed Web of Science ®Google Scholar
• Jeffery IB, O’Toole PW, Öhman L, Claesson MJ, Deane J, Quigley EM, Simrén M. An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota. Gut 2012; 61:997 - 1006; http://dx.doi.org/10.1136/gutjnl-2011-301501; PMID: 22180058
   PubMed Web of Science ®Google Scholar
• Carlisle EM, Poroyko V, Caplan MS, Alverdy J, Morowitz MJ, Liu D. Murine gut microbiota and transcriptome are diet dependent. Ann Surg 2013; 257:287 - 94; http://dx.doi.org/10.1097/SLA.0b013e318262a6a6; PMID: 23001074
   PubMed Web of Science ®Google Scholar
• Higashimura Y, Naito Y, Takagi T, Mizushima K, Hirai Y, Harusato A, Ohnogi H, Yamaji R, Inui H, Nakano Y, et al. Oligosaccharides from agar inhibit murine intestinal inflammation through the induction of heme oxygenase-1 expression. J Gastroenterol 2013; 48:897 - 909; http://dx.doi.org/10.1007/s00535-012-0719-4; PMID: 23188093
   PubMed Web of Science ®Google Scholar
• McHardy IH, Goudarzi M, Tong M, Ruegger PM, Schwager E, Weger JR, Graeber TG, Sonnenburg JL, Horvath S, Huttenhower C, et al. Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships. Microbiome 2013; 1:17; http://dx.doi.org/10.1186/2049-2618-1-17; PMID: 24450808
   PubMed Web of Science ®Google Scholar
• Semova I, Carten JD, Stombaugh J, Mackey LC, Knight R, Farber SA, Rawls JF. Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish. Cell Host Microbe 2012; 12:277 - 88; http://dx.doi.org/10.1016/j.chom.2012.08.003; PMID: 22980325
   PubMed Web of Science ®Google Scholar
• Ridlon JM, Alves JM, Hylemon PB, Bajaj JS. Cirrhosis, bile acids, and gut microbiota: Unraveling a complex relationship. Gut Microbes 2013; 4:4; http://dx.doi.org/10.4161/gmic.25723; PMID: 23851335
   PubMedGoogle Scholar
• Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 2011; 334:105 - 8; http://dx.doi.org/10.1126/science.1208344; PMID: 21885731
   PubMed Web of Science ®Google Scholar
• Gomara RE, Halata MS, Newman LJ, Bostwick HE, Berezin SH, Cukaj L, See MC, Medow MS. Fructose intolerance in children presenting with abdominal pain. J Pediatr Gastroenterol Nutr 2008; 47:303 - 8; http://dx.doi.org/10.1097/MPG.0b013e318166cbe4; PMID: 18728526
   PubMed Web of Science ®Google Scholar
• Irvine EJ, Whitehead WE, Chey WD, Matsueda K, Shaw M, Talley NJ, Veldhuyzen van Zanten SJ, Design of Treatment Trials Committee. Design of treatment trials for functional gastrointestinal disorders. Gastroenterology 2006; 130:1538 - 51; http://dx.doi.org/10.1053/j.gastro.2005.11.058; PMID: 16678567
   PubMed Web of Science ®Google Scholar
• Chumpitazi BP, Lane MM, Czyzewski DI, Weidler EM, Swank PR, Shulman RJ. Creation and initial evaluation of a Stool Form Scale for children. J Pediatr 2010; 157:594 - 7; http://dx.doi.org/10.1016/j.jpeds.2010.04.040; PMID: 20826285
   PubMed Web of Science ®Google Scholar
• Shulman RJ, Eakin MN, Jarrett M, Czyzewski DI, Zeltzer LK. Characteristics of pain and stooling in children with recurrent abdominal pain. J Pediatr Gastroenterol Nutr 2007; 44:203 - 8; http://dx.doi.org/10.1097/01.mpg.0000243437.39710.c0; PMID: 17255832
   PubMed Web of Science ®Google Scholar
• Lane MM, Czyzewski DI, Chumpitazi BP, Shulman RJ. Reliability and validity of a modified Bristol Stool Form Scale for children. J Pediatr 2011; 159:437 - 41, e1; http://dx.doi.org/10.1016/j.jpeds.2011.03.002; PMID: 21489557
   PubMed Web of Science ®Google Scholar
• Longstreth GF, Thompson WG, Chey WD, Houghton LA, Mearin F, Spiller RC. Functional bowel disorders. Gastroenterology 2006; 130:1480 - 91; http://dx.doi.org/10.1053/j.gastro.2005.11.061; PMID: 16678561
   PubMed Web of Science ®Google Scholar
• Shulman RJ, Kerzner B, Sloan HR, Boutton TW, Wong WW, Nichols BL, Klein PD. Absorption and oxidation of glucose polymers of different lengths in young infants. Pediatr Res 1986; 20:740 - 3; http://dx.doi.org/10.1203/00006450-198608000-00008; PMID: 3737286
   PubMed Web of Science ®Google Scholar
• Shulman RJ, Wong WW, Irving CS, Nichols BL, Klein PD. Utilization of dietary cereal by young infants. J Pediatr 1983; 103:23 - 8; http://dx.doi.org/10.1016/S0022-3476(83)80769-0; PMID: 6408235
   PubMed Web of Science ®Google Scholar
• Niu HC, Schoeller DA, Klein PD. Improved gas chromatographic quantitation of breath hydrogen by normalization to respiratory carbon dioxide. J Lab Clin Med 1979; 94:755 - 63; PMID: 501202
   PubMed Web of Science ®Google Scholar
• Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 2012; 486:207 - 14; http://dx.doi.org/10.1038/nature11234; PMID: 22699609
   PubMed Web of Science ®Google Scholar
• Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010; 7:335 - 6; http://dx.doi.org/10.1038/nmeth.f.303; PMID: 20383131
   PubMed Web of Science ®Google Scholar
• Riehle K, Coarfa C, Jackson A, Ma J, Tandon A, Paithankar S, Raghuraman S, Mistretta TA, Saulnier D, Raza S, et al. The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences. [abstract] BMC Bioinformatics 2012; 13:Suppl 13 S11; http://dx.doi.org/10.1186/1471-2105-13-S13-S11; PMID: 23320832
   PubMedGoogle Scholar
• Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006; 22:1658 - 9; http://dx.doi.org/10.1093/bioinformatics/btl158; PMID: 16731699
   PubMed Web of Science ®Google Scholar
• Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, et al, Human Microbiome Consortium. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 2011; 21:494 - 504; http://dx.doi.org/10.1101/gr.112730.110; PMID: 21212162
   PubMed Web of Science ®Google Scholar
• 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 - 7; http://dx.doi.org/10.1128/AEM.00062-07; PMID: 17586664
   PubMed Web of Science ®Google Scholar
• Montrose DC, Zhou XK, Kopelovich L, Yantiss RK, Karoly ED, Subbaramaiah K, Dannenberg AJ. Metabolic profiling, a noninvasive approach for the detection of experimental colorectal neoplasia. Cancer Prev Res (Phila) 2012; 5:1358 - 67; http://dx.doi.org/10.1158/1940-6207.CAPR-12-0160; PMID: 22961778
   PubMed Web of Science ®Google Scholar
• Evans AM, DeHaven CD, Barrett T, Mitchell M, Milgram E. Integrated, nontargeted ultrahigh performance liquid chromatography/electrospray ionization tandem mass spectrometry platform for the identification and relative quantification of the small-molecule complement of biological systems. Anal Chem 2009; 81:6656 - 67; http://dx.doi.org/10.1021/ac901536h; PMID: 19624122
   PubMed Web of Science ®Google Scholar
• Reitman ZJ, Jin G, Karoly ED, Spasojevic I, Yang J, Kinzler KW, He Y, Bigner DD, Vogelstein B, Yan H. Profiling the effects of isocitrate dehydrogenase 1 and 2 mutations on the cellular metabolome. Proc Natl Acad Sci U S A 2011; 108:3270 - 5; http://dx.doi.org/10.1073/pnas.1019393108; PMID: 21289278
   PubMed Web of Science ®Google Scholar
• Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. Metagenomic biomarker discovery and explanation. Genome Biol 2011; 12:R60; http://dx.doi.org/10.1186/gb-2011-12-6-r60; PMID: 21702898
   PubMed Web of Science ®Google Scholar
• Krzywinski M, Birol I, Jones SJ, Marra MA. Hive plots--rational approach to visualizing networks. Brief Bioinform 2012; 13:627 - 44; http://dx.doi.org/10.1093/bib/bbr069; PMID: 22155641
   PubMed Web of Science ®Google Scholar
• R Development Core Team. A language and environment for statistical computing. Vienna, Australia: R Foundation for Statistical Computing, 2010.
   Google Scholar