Structural changes in the gut microbiome of constipated patients

Physiological Genomics

Volumn 46, Issue 18, 2014, Pages 679-686

  Zhu, Lixin ^a   Liu, Wensheng ^a   Alkhouri, Razan ^a   Baker, Robert D ^a   Bard, Jonathan E ^a   Quigley, Eamonn M ^b   Baker, Susan S ^a  

^a UNIVERSITY AT BUFFALO   (United States)

^b HOUSTON METHODIST HOSPITAL   (United States)

Author keywords

Butyrate; Constipation; Microbiota; Prevotella

Indexed keywords

GENOMIC DNA; RNA 16S;

ADOLESCENT; ARTICLE; BACTERIAL STRAIN; BIFIDOBACTERIUM; CHILDHOOD OBESITY; CLINICAL ARTICLE; COMPARATIVE STUDY; CONSTIPATION; CONTROLLED CLINICAL TRIAL; CONTROLLED STUDY; CROSS-SECTIONAL STUDY; DIETARY INTAKE; FECES; FECES MICROFLORA; FEMALE; FIRMICUTES; FOOD FREQUENCY QUESTIONNAIRE; GENETIC VARIABILITY; GLOBAL CHANGE; HUMAN; INTESTINE FLORA; LACTOBACILLUS; MALE; MICROBIAL DIVERSITY; NONHUMAN; PILOT STUDY; POPULATION ABUNDANCE; PREVOTELLA; PYROSEQUENCING; QUANTITATIVE ANALYSIS; BIODIVERSITY; CASE CONTROL STUDY; CHILD; COMPLICATION; GASTROINTESTINAL TRACT; GENETICS; MICROBIOLOGY; MICROFLORA; OBESITY; PHYLOGENY;

ADOLESCENT; BIODIVERSITY; CASE-CONTROL STUDIES; CHILD; CONSTIPATION; FEMALE; GASTROINTESTINAL TRACT; HUMANS; MALE; MICROBIOTA; OBESITY; PHYLOGENY;

EID: 84907149871     PISSN: 10948341     EISSN: 15312267     Source Type: Journal    
DOI: 10.1152/physiolgenomics.00082.2014     Document Type: Article

References (52)

1. Aas JA, Paster BJ, Stokes LN, Olsen I, Dewhirst FE. Defining the normal bacterial flora of the oral cavity. J Clin Microbiol 43: 5721–5732, 2005.
2. Almac A, Elicora SS, Yumuk Z, Dundar V, Willke A. The relationship between chronic otitis media with effusion and surface and deep flora of hypertrophic adenoids. Int J Pediatr Otorhinolaryngol 73: 1438–1440, 2009.
3. Banaszkiewicz A, Szajewska H. Ineffectiveness of Lactobacillus GG as an adjunct to lactulose for the treatment of constipation in children: a double-blind, placebo-controlled randomized trial. J Pediatr 146: 364–369, 2005.
4. Barcelo A, Claustre J, Moro F, Chayvialle JA, Cuber JC, Plaisancie P. Mucin secretion is modulated by luminal factors in the isolated vascularly perfused rat colon. Gut 46: 218–224, 2000.
5. Binder HJ, Mehta P. Short-chain fatty acids stimulate active sodium and chloride absorption in vitro in the rat distal colon. Gastroenterology 96: 989–996, 1989.
6. Buzzard IM, Stanton CA, Figueiredo M, Fries EA, Nicholson R, Hogan CJ, Danish SJ. Development and reproducibility of a brief food frequency questionnaire for assessing the fat, fiber, and fruit and vegetable intakes of rural adolescents. J Am Diet Assoc 101: 1438–1446, 2001.
7. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26: 266–267, 2010.
8. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena 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 Meth 7: 335–336, 2010.
9. CDC. 2005 NHIS Questionnaire, ftp://ftp.cdc.gov/pub/Health_Statistics/ NCHS/Survey_Questionnaires/NHIS/2005/English/QCANCER.pdf (May 08, 2012).
10. Chao A. Non-parametric estimation of the number of classes in a population. Scand J Stat 11: 265–270, 1984.
11. Chiquette J, Allison MJ, Rasmussen MA. Prevotella bryantii 25A used as a probiotic in early-lactation dairy cows: effect on ruminal fermentation characteristics, milk production, and milk composition. J Dairy Sci 91: 3536–3543, 2008.
12. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam- Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141–D145, 2009.
13. Constipation Guideline Committee of the North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition. Evaluation and treatment of constipation in infants and children: recommendations of the North American Society for Pediatric Gastroenterology, Hepatology and Nutrition. J Pediatr Gastroenterol Nutr 43: e1–e13, 2006.
14. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G, Lionetti P. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci USA 107: 14691–14696, 2010.
15. Dehority BA. Characterization of several bovine rumen bacteria isolated with a xylan medium. J Bacteriol 91: 1724–1729, 1966.
16. Dukas L, Willett WC, Giovannucci EL. Association between physical activity, fiber intake, and other lifestyle variables and constipation in a study of women. Am J Gastroenterol 98: 1790–1796, 2003.
17. Faith DP, Baker AM. Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges. Evol Bioinform Online 2: 121–128, 2006.
18. Fishman L, Lenders C, Fortunato C, Noonan C, Nurko S. Increased prevalence of constipation and fecal soiling in a population of obese children. J Pediatr 145: 253–254, 2004.
19. Harding GK, Sutter VL, Finegold SM, Bricknell KS. Characterization of bacteroides melaninogenicus. J Clin Microbiol 4: 354–359, 1976.
20. Hayashi H, Shibata K, Sakamoto M, Tomita S, Benno Y. Prevotella copri sp. nov. and Prevotella stercorea sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 57: 941–946, 2007.
21. Hilty M, Burke C, Pedro H, Cardenas P, Bush A, Bossley C, Davies J, Ervine A, Poulter L, Pachter L, Moffatt MF, Cookson WO. Disordered microbial communities in asthmatic airways. PLoS One 5: e8578, 2010.
22. Hudson TS, Forman MR, Cantwell MM, Schatzkin A, Albert PS, Lanza E. Dietary fiber intake: assessing the degree of agreement between food frequency questionnaires and 4-day food records. J Am Coll Nutr 25: 370–381, 2006.
23. Hyman RW, Fukushima M, Diamond L, Kumm J, Giudice LC, Davis RW. Microbes on the human vaginal epithelium. Proc Natl Acad Sci USA 102: 7952–7957, 2005.
24. Johnson JL, Holdeman LV. Bacteroides intermedius comb. nov. and Descriptions of Bacteroides corporis sp. nov. and Bacteroides levii sp. nov. Int J Syst Bacteriol 33: 15–25, 1983.
25. Khalif IL, Quigley EM, Konovitch EA, Maximova ID. Alterations in the colonic flora and intestinal permeability and evidence of immune activation in chronic constipation. Dig Liver Dis 37: 838–849, 2005.
26. Kim G, Deepinder F, Morales W, Hwang L, Weitsman S, Chang C, Gunsalus R, Pimentel M. Methanobrevibacter smithii is the predominant methanogen in patients with constipation-predominant IBS and methane on breath. Dig Dis Sci 57: 3213–3218, 2012.
27. Koebnick C, Wagner I, Leitzmann P, Stern U, Zunft HJ. Probiotic beverage containing Lactobacillus casei Shirota improves gastrointestinal symptoms in patients with chronic constipation. Can J Gastroenterol 17: 655–659, 2003.
28. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature 444: 1022–1023, 2006.
29. Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228–8235, 2005.
30. Mazlyn MM, Nagarajah LH, Fatimah A, Norimah AK, Goh KL. Effects of a probiotic fermented milk on functional constipation: a randomized, double-blind, placebo-controlled study. J Gastroenterol Hepatol 28: 1141–1147, 2013.
31. Mugie SM, Benninga MA, Di Lorenzo C. Epidemiology of constipation in children and adults: a systematic review. Best Pract Res Clin Gastroenterol 25: 3–18, 2011.
32. Murray JA, Marietta EV, Barton SH, Taneja V, Mangalam A. Prevotella histicola preparations and the treatment of autoimmune conditions. United States patent application publication, 2012.
33. Nakaji S, Tokunaga S, Sakamoto J, Todate M, Shimoyama T, Umeda T, Sugawara K. Relationship between lifestyle factors and defecation in a Japanese population. Eur J Nutr 41: 244–248, 2002.
34. Ouwehand AC, Lagstrom H, Suomalainen T, Salminen S. Effect of probiotics on constipation, fecal azoreductase activity and fecal mucin content in the elderly. Ann Nutr Metab 46: 159–162, 2002.
35. Pashankar DS, Loening-Baucke V. Increased prevalence of obesity in children with functional constipation evaluated in an academic medical center. Pediatrics 116: e377–e380, 2005.
36. Pei Z, Bini EJ, Yang L, Zhou M, Francois F, Blaser MJ. Bacterial biota in the human distal esophagus. Proc Natl Acad Sci USA 101: 4250–4255, 2004.
37. Price LB, Liu CM, Johnson KE, Aziz M, Lau MK, Bowers J, Ravel J, Keim PS, Serwadda D, Wawer MJ, Gray RH. The effects of circumcision on the penis microbiome. PLoS One 5: e8422, 2010.
38. Price MN, Dehal PS, Arkin AP. FastTree 2–approximately maximumlikelihood trees for large alignments. PLoS One 5: e9490, 2010.
39. Pryde SE, Duncan SH, Hold GL, Stewart CS, Flint HJ. The microbiology of butyrate formation in the human colon. FEMS Microbiol Lett 217: 133–139, 2002.
40. Purushe J, Fouts DE, Morrison M, White BA, Mackie RI; North American Consortium for Rumen Bacteria, Coutinho PM, Henrissat B, Nelson KE. Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche. Microb Ecol 60: 721–729, 2010.
41. Riezzo G, Orlando A, D’Attoma B, Guerra V, Valerio F, Lavermicocca P, De Candia S, Russo F. Randomised clinical trial: efficacy of Lactobacillus paracasei-enriched artichokes in the treatment of patients with functional constipation–a double-blind, controlled, crossover study. Aliment Pharmacol Ther 35: 441–450, 2012.
42. Sakamoto M, Ohkuma M. Reclassification of Xylanibacter oryzae Ueki et al. 2006 as Prevotella oryzae comb nov, with an emended description of the genus Prevotella. Int J Syst Evol Microbiol 62: 2637–2642, 2012.
43. Schwiertz A, Taras D, Schafer K, Beijer S, Bos NA, Donus C, Hardt PD. Microbiota and SCFA in lean and overweight healthy subjects. Obesity 18: 190–195, 2010.
44. Squires PE, Rumsey RD, Edwards CA, Read NW. Effect of short-chain fatty acids on contractile activity and fluid flow in rat colon in vitro. Am J Physiol Gastrointest Liver Physiol 262: G813–G817, 1992.
45. Stephen AM, Cummings JH. The microbial contribution to human faecal mass. J Med Microbiol 13: 45–56, 1980.
46. Thompson F, Subar A. Dietary assessment methodology. In: Nutrition in the Prevention and Treatment of Disease, edited by Coulston A, Boushey C. San Diego, CA: Academic, 2008, p. 3–39.
47. van Gylswyk NO. Enumeration and presumptive identification of some functional groups of bacteria in the rumen of dairy cows fed grass silage-based diets. FEMS Microbiol Lett 73: 243–261, 1990.
48. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, 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 334: 105–108, 2011.
49. Yang L, Lu X, Nossa CW, Francois F, Peek RM, Pei Z. Inflammation and intestinal metaplasia of the distal esophagus are associated with alterations in the microbiome. Gastroenterology 137: 588–597, 2009.
50. Yousefi-Mashouf R, Eley A, Duerden BI. Characterisation of nonpigmented species of the genus Prevotella by polyacrylamide gel electrophoresis. J Med Microbiol 37: 83–90, 1992.
51. Zaura E, Keijser BJ, Huse SM, Crielaard W. Defining the healthy “core microbiome” of oral microbial communities. BMC Microbiol 9: 259, 2009.
52. Zoppi G, Cinquetti M, Luciano A, Benini A, Muner A, Bertazzoni Minelli E. The intestinal ecosystem in chronic functional constipation. Acta Paediatr 87: 836–841, 1998.