Diarrhoea-predominant Irritable Bowel Syndrome Distinguishable by 16S RRNA Gene Phylotype Quantification

Overview

Journal World J Gastroenterol

Publisher Baishideng Publishing Group

Specialty Gastroenterology

Date 2009 Dec 17

PMID 20014457

Citations 90

Authors

Anna Lyra

Teemu Rinttila

Janne Nikkila

Lotta Krogius-Kurikka

Kajsa Kajander

Erja Malinen

Jaana Matto

Laura Makela

Airi Palva

Affiliations

Soon will be listed here.

Abstract

Aim: To study whether selected bacterial 16S ribosomal RNA (rRNA) gene phylotypes are capable of distinguishing irritable bowel syndrome (IBS).

Methods: The faecal microbiota of twenty volunteers with IBS, subdivided into eight diarrhoea-predominant (IBS-D), eight constipation-predominant (IBS-C) and four mixed symptom-subtype (IBS-M) IBS patients, and fifteen control subjects, were analysed at three time-points with a set of fourteen quantitative real-time polymerase chain reaction assays. All assays targeted 16S rRNA gene phylotypes putatively associated with IBS, based on 16S rRNA gene library sequence analysis. The target phylotypes were affiliated with Actinobacteria, Bacteroidetes and Firmicutes. Eight of the target phylotypes had less than 95% similarity to cultured bacterial species according to their 16S rRNA gene sequence. The data analyses were made with repeated-measures ANCOVA-type modelling of the data and principle component analysis (PCA) with linear mixed-effects models applied to the principal component scores.

Results: Bacterial phylotypes Clostridium cocleatum 88%, Clostridium thermosuccinogenes 85%, Coprobacillus catenaformis 91%, Ruminococcus bromii-like, Ruminococcus torques 91%, and R. torques 93% were detected from all samples analysed. A multivariate analysis of the relative quantities of all 14 bacterial 16S rRNA gene phylotypes suggested that the intestinal microbiota of the IBS-D patients differed from other sample groups. The PCA on the first principal component (PC1), explaining 30.36% of the observed variation in the IBS-D patient group, was significantly altered from all other sample groups (IBS-D vs control, P = 0.01; IBS-D vs IBS-M, P = 0.00; IBS-D vs IBS-C, P = 0.05). Significant differences were also observed in the levels of distinct phylotypes using relative values in proportion to the total amount of bacteria. A phylotype with 85% similarity to C. thermosuccinogenes was quantified in significantly different quantities among the IBS-D and control subjects (-4.08 +/- 0.90 vs -3.33 +/- 1.16, P = 0.04) and IBS-D and IBS-M subjects (-4.08 +/- 0.90 vs -3.08 +/- 1.38, P = 0.05). Furthermore, a phylotype with 94% similarity to R. torques was more prevalent in IBS-D patients' intestinal microbiota than in that of control subjects (-2.43 +/- 1.49 vs -4.02 +/- 1.63, P = 0.01). A phylotype with 93% similarity to R. torques was associated with control samples when compared with IBS-M (-2.41 +/- 0.53 vs -2.92 +/- 0.56, P = 0.00). Additionally, a R. bromii-like phylotype was associated with IBS-C patients in comparison to control subjects (-1.61 +/- 1.83 vs -3.69 +/- 2.42, P = 0.01). All of the above mentioned phylotype specific alterations were independent of the effect of time.

Conclusion: Significant phylotype level alterations in the intestinal microbiotas of IBS patients were observed, further emphasizing the possible contribution of the gastrointestinal microbiota in IBS.

Citing Articles

The Impact of Hangeshashinto on Symptoms and Gut Microbiota in Diarrhea-type Irritable Bowel Syndrome: A Retrospective Analysis.

Yoshida N, Yasuda T, Inagaki Y, Hasegawa D, Fukumoto K, Murakami T J Anus Rectum Colon. 2025; 9(1):105-116.

PMID: 39882236 PMC: 11772784. DOI: 10.23922/jarc.2024-068.

The effect of workplace environment on coal miners' gut microbiota in a mouse model.

Li L, Zhi M, Wang S, Deng J, Cai Q, Feng D Front Microbiol. 2024; 15:1453798.

PMID: 39723143 PMC: 11668784. DOI: 10.3389/fmicb.2024.1453798.

Consumption of resistant potato starch produces changes in gut microbiota that correlate with improvements in abnormal bowel symptoms: a secondary analysis of a clinical trial.

Bush J, Alfa M BMC Nutr. 2024; 10(1):152.

PMID: 39605008 PMC: 11600726. DOI: 10.1186/s40795-024-00962-7.

Effect of Personalized Prebiotic and Probiotic Supplements on the Symptoms of Irritable Bowel Syndrome: An Open-Label, Single-Arm, Multicenter Clinical Trial.

Matsuura N, Kanayama M, Watanabe Y, Yamada H, Lili L, Torii A Nutrients. 2024; 16(19).

PMID: 39408300 PMC: 11478705. DOI: 10.3390/nu16193333.

Lactiplantibacillus plantarum P9 for chronic diarrhea in young adults: a large double-blind, randomized, placebo-controlled trial.

Yang N, Ma T, Xie Y, Li Q, Li Y, Zheng L Nat Commun. 2024; 15(1):6823.

PMID: 39122704 PMC: 11315937. DOI: 10.1038/s41467-024-51094-2.

References

Louis P, Duncan S, McCrae S, Millar J, Jackson M, Flint H . Restricted distribution of the butyrate kinase pathway among butyrate-producing bacteria from the human colon. J Bacteriol. 2004; 186(7):2099-106. PMC: 374397. DOI: 10.1128/JB.186.7.2099-2106.2004. View

HOSKINS L, Agustines M, McKee W, Boulding E, Kriaris M, Niedermeyer G . Mucin degradation in human colon ecosystems. Isolation and properties of fecal strains that degrade ABH blood group antigens and oligosaccharides from mucin glycoproteins. J Clin Invest. 1985; 75(3):944-53. PMC: 423632. DOI: 10.1172/JCI111795. View

Maukonen J, Satokari R, Matto J, Soderlund H, Mattila-Sandholm T, Saarela M . Prevalence and temporal stability of selected clostridial groups in irritable bowel syndrome in relation to predominant faecal bacteria. J Med Microbiol. 2006; 55(Pt 5):625-633. DOI: 10.1099/jmm.0.46134-0. View

Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermudez-Humaran L, Gratadoux J . Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A. 2008; 105(43):16731-6. PMC: 2575488. DOI: 10.1073/pnas.0804812105. View

Ley R, Turnbaugh P, Klein S, Gordon J . Microbial ecology: human gut microbes associated with obesity. Nature. 2006; 444(7122):1022-3. DOI: 10.1038/4441022a. View

Turnbaugh P, Hamady M, Yatsunenko T, Cantarel B, Duncan A, Ley R . A core gut microbiome in obese and lean twins. Nature. 2008; 457(7228):480-4. PMC: 2677729. DOI: 10.1038/nature07540. View

Gecse K, Roka R, Ferrier L, Leveque M, Eutamene H, Cartier C . Increased faecal serine protease activity in diarrhoeic IBS patients: a colonic lumenal factor impairing colonic permeability and sensitivity. Gut. 2008; 57(5):591-9. DOI: 10.1136/gut.2007.140210. View

Hayashi H, Sakamoto M, Benno Y . Phylogenetic analysis of the human gut microbiota using 16S rDNA clone libraries and strictly anaerobic culture-based methods. Microbiol Immunol. 2002; 46(8):535-48. DOI: 10.1111/j.1348-0421.2002.tb02731.x. View

Balsari A, Ceccarelli A, Dubini F, Fesce E, Poli G . The fecal microbial population in the irritable bowel syndrome. Microbiologica. 1982; 5(3):185-94. View

10.

Frank D, St Amand A, Feldman R, Boedeker E, Harpaz N, Pace N . Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A. 2007; 104(34):13780-5. PMC: 1959459. DOI: 10.1073/pnas.0706625104. View

11.

Matsuki T, Watanabe K, Fujimoto J, Takada T, Tanaka R . Use of 16S rRNA gene-targeted group-specific primers for real-time PCR analysis of predominant bacteria in human feces. Appl Environ Microbiol. 2004; 70(12):7220-8. PMC: 535136. DOI: 10.1128/AEM.70.12.7220-7228.2004. View

12.

Gill S, Pop M, DeBoy R, Eckburg P, Turnbaugh P, Samuel B . Metagenomic analysis of the human distal gut microbiome. Science. 2006; 312(5778):1355-9. PMC: 3027896. DOI: 10.1126/science.1124234. View

13.

Schloss P, Handelsman J . Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol. 2005; 71(3):1501-6. PMC: 1065144. DOI: 10.1128/AEM.71.3.1501-1506.2005. View

14.

Rozen S, Skaletsky H . Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol. 1999; 132:365-86. DOI: 10.1385/1-59259-192-2:365. View

15.

Moore W, Holdeman L . Human fecal flora: the normal flora of 20 Japanese-Hawaiians. Appl Microbiol. 1974; 27(5):961-79. PMC: 380185. DOI: 10.1128/am.27.5.961-979.1974. View

16.

McWilliam Leitch E, Walker A, Duncan S, Holtrop G, Flint H . Selective colonization of insoluble substrates by human faecal bacteria. Environ Microbiol. 2007; 9(3):667-79. DOI: 10.1111/j.1462-2920.2006.01186.x. View

17.

Roka R, Rosztoczy A, Leveque M, Izbeki F, Nagy F, Molnar T . A pilot study of fecal serine-protease activity: a pathophysiologic factor in diarrhea-predominant irritable bowel syndrome. Clin Gastroenterol Hepatol. 2007; 5(5):550-5. DOI: 10.1016/j.cgh.2006.12.004. View

18.

Li M, Wang B, Zhang M, Rantalainen M, Wang S, Zhou H . Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci U S A. 2008; 105(6):2117-22. PMC: 2538887. DOI: 10.1073/pnas.0712038105. View

19.

Kassinen A, Krogius-Kurikka L, Makivuokko H, Rinttila T, Paulin L, Corander J . The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects. Gastroenterology. 2007; 133(1):24-33. DOI: 10.1053/j.gastro.2007.04.005. View

20.

Spiller R . Role of infection in irritable bowel syndrome. J Gastroenterol. 2007; 42 Suppl 17:41-7. DOI: 10.1007/s00535-006-1925-8. View