Randomised clinical trial: gut microbiome biomarkers are associated with clinical response to a low FODMAP diet in children with the irritable bowel syndrome

Alimentary Pharmacology and Therapeutics

Volumn 42, Issue 4, 2015, Pages 418-427

  Chumpitazi, B P ^a   Cope, J L ^a,c   Hollister, E B ^a,c   Tsai, C M ^a   McMeans, A R ^b   Luna, R A ^a,c   Versalovic, J ^a,c   Shulman, R J ^a,b  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b CHILDREN S NUTRITION RESEARCH CENTER   (United States)

^c TEXAS CHILDREN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; DISACCHARIDE; MONOSACCHARIDE; OLIGOSACCHARIDE; POLYOL; RNA 16S; POLYMER;

ABDOMINAL PAIN; ADOLESCENT; ARTICLE; BACTEROIDES; CARBOHYDRATE METABOLISM; CHILD; CLINICAL ARTICLE; CLINICAL EFFECTIVENESS; CONTROLLED STUDY; CROSSOVER PROCEDURE; DIET THERAPY; DISEASE ASSOCIATION; DOUBLE BLIND PROCEDURE; FAECALIBACTERIUM PRAUSNITZII; FEMALE; FERMENTABLE OLIGOSACCHARIDES DISACCHARIDES MONOSACCHARIDES AND POLYOL DIET; FERMENTATION; HUMAN; INTESTINE FLORA; IRRITABLE COLON; MALE; METABOLIC CAPACITY; METAGENOMICS; PILOT STUDY; PRIORITY JOURNAL; RANDOMIZED CONTROLLED TRIAL; RNA SEQUENCE; RUMINOCOCCACEAE; THERAPY EFFECT; METABOLISM; MICROBIOLOGY;

ABDOMINAL PAIN; ADOLESCENT; BIOMARKERS; CHILD; CROSS-OVER STUDIES; DISACCHARIDES; DOUBLE-BLIND METHOD; FEMALE; FERMENTATION; GASTROINTESTINAL MICROBIOME; HUMANS; IRRITABLE BOWEL SYNDROME; MALE; MONOSACCHARIDES; OLIGOSACCHARIDES; POLYMERS; RNA, RIBOSOMAL, 16S;

EID: 84932107709     PISSN: 02692813     EISSN: 13652036     Source Type: Journal    
DOI: 10.1111/apt.13286     Document Type: Article

References (51)

1. Self MM, Czyzewski DI, Chumpitazi BP, et al. Subtypes of irritable bowel syndrome in children and adolescents. Clin Gastroenterol Hepatol 2014; 12: 1468–73.
2. Carlson MJ, Moore CE, Tsai CM, et al. Child and parent perceived food-induced gastrointestinal symptoms and quality of life in children with functional gastrointestinal disorders. J Acad Nutr Diet 2014; 114: 403–13.
3. Barr RG, Levine MD, Watkins JB. Recurrent abdominal pain of childhood due to lactose intolerance. N Engl J Med 1979; 300: 1449–52.
4. Dainese R, Casellas F, Marine-Barjoan E, et al. Perception of lactose intolerance in irritable bowel syndrome patients. Eur J Gastroenterol Hepatol 2014; 26: 1167–75.
5. Vos MB, Kimmons JE, Gillespie C, et al. Dietary fructose consumption among US children and adults: the Third National Health and Nutrition Examination Survey. Medscape J Med 2008; 10: 160.
6. Huertas-Ceballos AA, Logan S, Bennett C, et al. Dietary interventions for recurrent abdominal pain (RAP) and irritable bowel syndrome (IBS) in childhood. Cochrane Database Syst Rev 2009; (1): CD003019.
7. Halmos EP, Power VA, Shepherd SJ, et al. A diet low in FODMAPs reduces symptoms of irritable bowel syndrome. Gastroenterology 2014; 146: 67–75.
8. Ong DK, Mitchell SB, Barrett JS, et al. 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.
9. Gibson PR, Shepherd SJ. Food choice as a key management strategy for functional gastrointestinal symptoms. Am J Gastroenterol 2012; 107: 657–66.
10. 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. Epub 2006/09/27.
11. Murray K, Wilkinson-Smith V, Hoad C, et al. Differential effects of FODMAPs (fermentable oligo-, di-, mono-saccharides and polyols) on small and large intestinal contents in healthy subjects shown by MRI. Am J Gastroenterol 2014; 109: 110–9.
12. Halmos EP, Christophersen CT, Bird AR, et al. Diets that differ in their FODMAP content alter the colonic luminal microenvironment. Gut 2015; 64: 93–100.
13. Staudacher HM, Lomer MC, Anderson JL, et al. Fermentable carbohydrate restriction reduces luminal bifidobacteria and gastrointestinal symptoms in patients with irritable bowel syndrome. J Nutr 2012; 142: 1510–8.
14. de Roest RH, Dobbs BR, Chapman BA, et al. The low FODMAP diet improves gastrointestinal symptoms in patients with irritable bowel syndrome: a prospective study. Int J Clin Pract 2013; 67: 895–903.
15. Chumpitazi BP, Hollister EB, Oezguen N, et al. Gut microbiota influences low fermentable substrate diet efficacy in children with irritable bowel syndrome. Gut Microbes 2014; 5: 165–75.
16. Saulnier DM, Riehle K, Mistretta TA, et al. Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology 2011; 141: 1782–91.
17. Shulman RJ, Eakin MN, Jarrett M, et al. Characteristics of pain and stooling in children with recurrent abdominal pain. J Pediatr Gastroenterol Nutr 2007; 44: 203–8.
18. Chumpitazi BP, Lane MM, Czyzewski DI, et al. Creation and initial evaluation of a Stool Form Scale for children. J Pediatr 2010; 157: 594–7.
19. Human Microbiome Project C. Structure function and diversity of the healthy human microbiome. Nature 2012; 486: 207–14.
20. Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010; 7: 335–6.
21. Haas BJ, Gevers D, Earl AM, et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 2011; 21: 494–504.
22. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010; 26: 2460–1.
23. DeSantis TZ, Hugenholtz P, Larsen N, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006; 72: 5069–72.
24. Langille MG, Zaneveld J, Caporaso JG, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnol 2013; 31: 814–21.
25. Kanehisa M, Goto S, Sato Y, et al. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 2012; 40(Database issue): D109–14.
26. Vlieger AM, Menko-Frankenhuis C, Wolfkamp SC, et al. Hypnotherapy for children with functional abdominal pain or irritable bowel syndrome: a randomized controlled trial. Gastroenterology 2007; 133: 1430–6.
27. Enck P, Horing B, Weimer K, et al. Placebo responses and placebo effects in functional bowel disorders. Eur J Gastroenterol Hepatol 2012; 24: 1–8.
28. Enck P, Klosterhalfen S, Weimer K, et al. The placebo response in clinical trials: more questions than answers. Philos Trans R Soc Lond B Biol Sci 2011; 366: 1889–95.
29. Irvine EJ, Whitehead WE, Chey WD, et al. Design of treatment trials for functional gastrointestinal disorders. Gastroenterology 2006; 130: 1538–51.
30. Segata N, Izard J, Waldron L, et al. Metagenomic biomarker discovery and explanation. Genome Biol 2011; 12: R60.
31. Ma J, Prince AL, Bader D, et al. High-fat maternal diet during pregnancy persistently alters the offspring microbiome in a primate model. Nature Commun 2014; 5: 3889.
32. Saeed F, Pasha I, Anjum FM, et al. Arabinoxylans and arabinogalactans: a comprehensive treatise. Crit Rev Food Sci Nutr 2011; 51: 467–76.
33. Rao SS, Yu S, Fedewa A. Systematic review: dietary fibre and FODMAP-restricted diet in the management of constipation and irritable bowel syndrome. Aliment Pharmacol Ther 2015; 41: 1256–70.
34. Lomer MC. Review article: the aetiology, diagnosis, mechanisms and clinical evidence for food intolerance. Aliment Pharmacol Ther 2015; 41: 262–75.
35. Flint HJ, Scott KP, Duncan SH, et al. Microbial degradation of complex carbohydrates in the gut. Gut Microbes 2012; 3: 289–306.
36. Taras D, Simmering R, Collins MD, et al. 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(Pt 2): 423–8.
37. Varela E, Manichanh C, Gallart M, et al. Colonisation by Faecalibacterium prausnitzii and maintenance of clinical remission in patients with ulcerative colitis. Aliment Pharmacol Ther 2013; 38: 151–61.
38. Miquel S, Martin R, Rossi O, et al. Faecalibacterium prausnitzii and human intestinal health. Curr Opin Microbiol 2013; 16: 255–61.
39. Mao S, Zhang R, Wang D, et al. The diversity of the fecal bacterial community and its relationship with the concentration of volatile fatty acids in the feces during subacute rumen acidosis in dairy cows. BMC Vet Res 2012; 8: 237.
40. Everard A, Lazarevic V, Gaia N, et al. Microbiome of prebiotic-treated mice reveals novel targets involved in host response during obesity. ISME J 2014; 8: 2116–30.
41. Bosshard PP, Zbinden R, Altwegg M. Turicibacter sanguinis gen. nov., sp. nov., a novel anaerobic, Gram-positive bacterium. Int J Syst Evol Microbiol 2002; 52(Pt 4): 1263–6.
42. Dupont HL. Review article: evidence for the role of gut microbiota in irritable bowel syndrome and its potential influence on therapeutic targets. Aliment Pharmacol Ther 2014; 39: 1033–42.
43. Wang ZK, Yang YS, Stefka AT, et al. Review article: fungal microbiota and digestive diseases. Aliment Pharmacol Ther 2014; 39: 751–66.
44. Ravcheev DA, Khoroshkin MS, Laikova ON, et al. Comparative genomics and evolution of regulons of the LacI-family transcription factors. Front Microbiol 2014; 5: 294.
45. O'Connell KJ, Motherway MO, Liedtke A, et al. Transcription of two adjacent carbohydrate utilization gene clusters in Bifidobacterium breve UCC2003 is controlled by LacI- and repressor open reading frame kinase (ROK)-type regulators. Appl Environ Microbiol 2014; 80: 3604–14.
46. Rajilic-Stojanovic M, Jonkers DM, Salonen A, et al. Intestinal microbiota and diet in IBS: causes, consequences, or epiphenomena? Am J Gastroenterol 2015; 110: 278–87.
47. Shepherd SJ, Lomer MC, Gibson PR. Short-chain carbohydrates and functional gastrointestinal disorders. Am J Gastroenterol 2013; 108: 707–17.
48. Yang J, Fox M, Cong Y, et al. Lactose intolerance in irritable bowel syndrome patients with diarrhoea: the roles of anxiety, activation of the innate mucosal immune system and visceral sensitivity. Aliment Pharmacol Ther 2014; 39: 302–11.
49. Enck P, Klosterhalfen S, Zipfel S. Novel study designs to investigate the placebo response. BMC Med Res Methodol 2011; 11: 90.
50. Goodrich JK, Di Rienzi SC, Poole AC, et al. Conducting a microbiome study. Cell 2014; 158: 250–62.
51. David LA, Maurice CF, Carmody RN, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014; 505: 559–63.