Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

Gut

Volumn 65, Issue 1, 2016, Pages 57-62

  Vandeputte, Doris ^a,b,c   Falony, Gwen ^a,b   Vieira Silva, Sara ^a,b   Tito, Raul Y ^a,b,c   Joossens, Marie ^a,b,c   Raes, Jeroen ^a,b,c  

^a REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

^b DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^c VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; AKKERMANSIA; ARTICLE; BACTERIAL GENETICS; BACTERIAL GROWTH; BACTEROIDETES; BRISTOL STOOL SCALE CLASSIFICATION; BUTYRICIMONAS; CODING AND CLASSIFICATION; DIGESTIVE TRACT PARAMETERS; FECES ANALYSIS; FEMALE; FIRMICUTES; HUMAN; HUMAN EXPERIMENT; INTESTINE FLORA; INTESTINE TRANSIT TIME; METAGENOME; METHANOBREVIBACTER; METHANOSPHAERA; NONHUMAN; NORMAL HUMAN; ODORIBACTER; OXALOBACTER; POPULATION ABUNDANCE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SPECIES COMPOSITION; SPECIES RICHNESS; STOOL CONSISTENCY; FECES; GASTROINTESTINAL TRANSIT; MICROBIOLOGY; MIDDLE AGED; PHYSIOLOGY; SELF REPORT;

ADULT; FECES; FEMALE; GASTROINTESTINAL MICROBIOME; GASTROINTESTINAL TRANSIT; HEALTHY VOLUNTEERS; HUMANS; MIDDLE AGED; SELF REPORT;

EID: 84952942226     PISSN: 00175749     EISSN: 14683288     Source Type: Journal    
DOI: 10.1136/gutjnl-2015-309618     Document Type: Article

References (50)

1. Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010;464:59-65.
2. Gevers D, Knight R, Petrosino JF, et al. The Human Microbiome Project: a community resource for the healthy human microbiome. PLoS Biol 2012;10:e1001377.
3. Costello EK, Lauber CL, Hamady M, et al. Bacterial community variation in human body habitats across space and time. Science 2009;326:1694-7.
4. Brown J, de Vos WM, DiStefano PS, et al. Translating the human microbiome. Nat Biotechnol 2013;31:304-8.
5. Wu GD, Chen J, Hoffmann C, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 2011;334:105-8.
6. David LA, Maurice CF, Carmody RN, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014;505:559-63.
7. Cho I, Yamanishi S, Cox L, et al. Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature 2012;488:621-6.
8. Le Chatelier E, Nielsen T, Qin J, et al. Richness of human gut microbiome correlates with metabolic markers. Nature 2013;500:541-6.
9. Hildebrand F, Nguyen TLA, Brinkman B, et al. Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice. Genome Biol 2013;14:R4.
10. Lewis SJ, Heaton KW. Stool form scale as a useful guide to intestinal transit time. Scand J Gastroenterol 1997;32:920-4.
11. Heaton KW, Radvan J, Cripps H, et al. Defecation frequency and timing, and stool form in the general population: a prospective study. Gut 1992;33:818-24.
12. Degen LP, Phillips SF. How well does stool form reflect colonic transit? Gut 1996;39:109-13.
13. Longstreth GF, Thompson WG, Chey WD, et al. Functional Bowel Disorders. Gastroenterology 2006;130:1480-91.
14. Videlock EJ, Cheng V, Cremonini F. Effects of linaclotide in patients with irritable bowel syndrome with constipation or chronic constipation: a meta-analysis. Clin Gastroenterol Hepatol 2013;11:1084-92.
15. Collado Yurrita L, San Mauro Martín I, Ciudad-Cabañas MJ, et al. Effectiveness of inulin intake on indicators of chronic constipation; a meta-analysis of controlled randomized clinical trials. Nutr Hosp 2014;30:244-52.
16. Saad RJ, Rao SSC, Koch KL, et al. Do stool form and frequency correlate with whole-gut and colonic transit? Results from a multicenter study in constipated individuals and healthy controls. Am J Gastroenterol 2010;105:403-11.
17. Schiraldi A, Fessas D, Signorelli M. Water activity in biological systems - a review. Polish J Food Nutr Sci 2012;62:5-13.
18. Degen LP, Phillips SF. Variability of gastrointestinal transit in healthy women and men. Gut 1996;39:299-305.
19. Godon JJ, Zumstein E, Dabert P, et al. Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl Environ Microbiol 1997;63:2802-13.
20. Aronesty E. Comparison of Sequencing Utility Programs. Open Bioinforma J 2013;7:1-8.
21. Maechler AM, Analysis DC, Struyf A. cluster: Cluster Analysis Basics and Extensions. R package version 1.14.4. 2013.
22. Holmes I, Harris K, Quince C. Dirichlet multinomial mixtures: generative models for microbial metagenomics. PLoS ONE 2012;7:e30126.
23. Arumugam M, Raes J, Pelletier E, et al. Enterotypes of the human gut microbiome. Nature 2011;473:174-80.
24. McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 2013;8:e61217.
25. Vieira-Silva S, Rocha EPC. The systemic imprint of growth and its uses in ecological (meta)genomics. PLoS Genet 2010;6:e1000808.
26. Lozupone CA, Stombaugh JI, Gordon JI, et al. Diversity, stability and resilience of the human gut microbiota. Nature 2012;489:220-30.
27. Cho I, Blaser MJ. The human microbiome: at the interface of health and disease. Nat Rev Genet 2012;13:260-70.
28. Gorkiewicz G, Thallinger G, Trajanoski S. Alterations in the colonic microbiota in response to osmotic diarrhea. PLoS ONE 2013;8:e55817.
29. Yatsunenko T, Rey FE, Manary MJ, et al. Human gut microbiome viewed across age and geography. Nature 2012;486:222-7.
30. Salonen A, de Vos WM. Impact of diet on human intestinal microbiota and health. Annu Rev Food Sci Technol 2014;5:239-62.
31. De Filippo C, Cavalieri D, Di Paola M, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci USA 2010;107:14691-6.
32. Mudgil D, Barak S. Composition, properties and health benefits of indigestible carbohydrate polymers as dietary fiber: a review. Int J Biol Macromol 2013;61:1-6.
33. Sahakian AB, Jee S-R, Pimentel M. Methane and the gastrointestinal tract. Dig Dis Sci 2010;55:2135-43.
34. Pimentel M, Lin HC, Enayati P, et al. Methane, a gas produced by enteric bacteria, slows intestinal transit and augments small intestinal contractile activity. Am J Physiol Gastrointest Liver Physiol 2006;290:1089-95.
35. Flint H, Duncan S, Scott KP, et al. Interactions and competition within the microbial community of the human colon: links between diet and health. Environ Microbiol 2007;9:1101-11.
36. Koch a L. Oligotrophs versus copiotrophs. Bioessays 2001;23:657-61.
37. James TW. Continous culture of microorganisms. Annu Rev Microbiol 1960:27-46.
38. Hobson PN. Continuous culture of some anerobic and facultatively anaerobic rumen bacteria. J Gen Microbiol 1965;38:167-80.
39. Isaacson HR, Hinds FC, Bryant MP, et al. Efficiency of energy utilization by mixed rumen bacteria in continuous culture. J Dairy Sci 1975;58:1645-59.
40. Stephen a M, Wiggins HS, Cummings JH. Effect of changing transit time on colonic microbial metabolism in man. Gut 1987;28:601-9.
41. Stephen M, Cummings JH. The microbial contribution to human fecal mass. J Med Microbiol 1980;13:45-56.
42. Grenier D. Collagen-binding activity of Prevotella intermedia measured by a microtitre plate adherence assay. Microbiology 1996;142:1537-41.
43. Wright D, Rosendale D, Robertson A. Prevotella enzymes involved in mucin oligosaccharide degradation and evidence for a small operon of genes expressed during growth on mucin. FEMS Microbiol Lett 2000;190:73-9.
44. Santiago A, Panda S, Mengels G, et al. Processing faecal samples: a step forward for standards in microbial community analysis. BMC Microbiol 2014;14:112.
45. Scheperjans F, Aho V, Pereira P a. B, et al. Gut microbiota are related to Parkinson's disease and clinical phenotype. Mov Disord 2014;30:350-8.
46. Kaye J, Gage H, Kimber A, et al. Excess burden of constipation in Parkinson's disease: a pilot study. Mov Disord 2006;21:1270-3.
47. Agachan F, Chen T, Pfeifer J, et al. A constipation scoring system to simplify evaluation and management of constipated patients. Dis Colon Rectum 1996;39:681-5.
48. Lewis SJ, Heaton KW. Increasing butyrate concentration in the distal colon by accelerating intestinal transit. Gut 1997;41:245-51.
49. Lewis SJ, Heaton KW. The metabolic consequences of slow colonic transit. Am J Gastroenterol 1999;94:2010-16.
50. Burkitt D, Walker A, Painter N. Effect of dietary fibre on stools and transit times and its role in the causation of disease. Lancet 1972;300:1408-11.