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Cited by 227Gut microbiota and healthInflammatory Bowel DiseaseGastrointestinal motility and disorders

The DOI matches its Crossref record; 56 of the 56 references it cites were found in a registry or an index.

Ulcerative colitis and irritable bowel patients exhibit distinct abnormalities of the gut microbiota

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Noor, Samah O, Ridgway, Karyn, Scovell, Louise, Kemsley, E Katherine, Lund, Elizabeth K, Jamieson, Crawford, Johnson, Ian T, Narbad, Arjan·2010·BMC Gastroenterology
DOI 10.1186/1471-230x-10-134PMC PMC3002299
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Abstract

Background: Previous studies suggest a link between gut microbiota and the development of ulcerative colitis (UC) and irritable bowel syndrome (IBS). Our aim was to investigate any quantitative differences in faecal bacterial compositions in UC and IBS patients compared to healthy controls, and to identify individual bacterial species that contribute to these differences. Methods: Faecal microbiota of 13 UC patients, 11 IBS patients and 22 healthy volunteers were analysed by PCR-Denaturing Gradient Gel Electrophoresis (DGGE) using universal and Bacteroides specific primers. The data obtained were normalized using in-house developed statistical method and interrogated by multivariate approaches. The differentiated bands were excised and identified by sequencing the V3 region of the 16S rRNA genes. Results: Band profiles revealed that number of predominant faecal bacteria were significantly different between UC, IBS and control group (p < 10-4). By assessing the mean band numbers in UC (37 ± 5) and IBS (39 ± 6), compared to the controls (45 ± 3), a significant decrease in bacterial species is suggested (p = 0.01). There were no significant differences between IBS and UC. Biodiversity of the bacterial species was significantly lower in UC (μ = 2.94, σ = 0.29) and IBS patients (μ = 2.90, σ = 0.38) than controls (μ = 3.25, σ = 0.16; p = 0.01). Moreover, similarity indices revealed greater biological variability of predominant bacteria in UC and IBS compared to the controls (median Dice coefficients 76.1% (IQR 70.9 - 83.1), 73.8% (IQR 67.0 - 77.5) and 82.9% (IQR 79.1 - 86.7) respectively). DNA sequencing of discriminating bands suggest that the presence of Bacteroides vulgatus, B. ovatus, B. uniformis, and Parabacteroides sp. in healthy volunteers distinguishes them from IBS and UC patients. DGGE profiles of Bacteroides species revealed a decrease of Bacteroides community in UC relative to IBS and controls. Conclusion: Molecular profiling of faecal bacteria revealed abnormalities of intestinal microbiota in UC and IBS patients, while different patterns of Bacteroides species loss in particular, were associated with UC and IBS.

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Figure 1 DGGE profiles and band numbers. (a) DGGE profiles of faecal samples obtained from IBS, UC and control subjects showing the number of bands corresponding to amplicons of the V3 region of 16S rRNA of faecal bacteria. (b) Box plots presenting the median and range of band counts of all faecal samples taken from UC, IBS, and controls. (Boxes have lines at the lower quartile, median, and upper quartile values; whiskers show extent of the rest of the data. Notches display the variability of the median between samples; notches that do not overlap have different medians at the 5% significance level).
Figure 1 DGGE profiles and band numbers. (a) DGGE profiles of faecal samples obtained from IBS, UC and control subjects showing the number of bands corresponding to amplicons of the V3 region of 16S rRNA of faecal bacteria. (b) Box plots presenting the median and range of band counts of all faecal samples taken from UC, IBS, and controls. (Boxes have lines at the lower quartile, median, and upper quartile values; whiskers show extent of the rest of the data. Notches display the variability of the median between samples; notches that do not overlap have different medians at the 5% significance level).CC BY · PubMed Central
Figure 2 Synthetic Standards (SS) alignment. SS lanes from a single typical gel, (a) before alignment and (b) after alignment, showing relative stretching and shrinking of piecewise regions in the bespoke alignment routine. Images of all SS lanes from all gels: (c) before, and (d) after the complete alignment procedure.
Figure 2 Synthetic Standards (SS) alignment. SS lanes from a single typical gel, (a) before alignment and (b) after alignment, showing relative stretching and shrinking of piecewise regions in the bespoke alignment routine. Images of all SS lanes from all gels: (c) before, and (d) after the complete alignment procedure.CC BY · PubMed Central
Figure 3 Statistical analysis of DGGE profiles. (a) Classification success rate (cross-validated) versus number of PLS dimensions used. A local maximum of ~64% was obtained from a 4-factor model. Also shown are compact boxplots summarizing the results of PLS-DA permutation tests (using y-scrambling, 10,000 re-samples). (b) CVA scores plot derived from PLS scores (4 dimensions) of the DGGE data of faecal bacteria showing the relative positions of the UC, IBS, and control groups. (NB: fully-leave-sample-out cross-validated.)
Figure 3 Statistical analysis of DGGE profiles. (a) Classification success rate (cross-validated) versus number of PLS dimensions used. A local maximum of ~64% was obtained from a 4-factor model. Also shown are compact boxplots summarizing the results of PLS-DA permutation tests (using y-scrambling, 10,000 re-samples). (b) CVA scores plot derived from PLS scores (4 dimensions) of the DGGE data of faecal bacteria showing the relative positions of the UC, IBS, and control groups. (NB: fully-leave-sample-out cross-validated.)CC BY · PubMed Central
Figure 4 Bands analysis of DGGE profiles. (a) Absolute values of first PLS loading, peak-picked to show bands that are most responsible for distinguishing between the groups. Greyed area indicates range of this loading across the training segments. (b) Greyscale image view of complete aligned dataset, on the same Rf axis.
Figure 4 Bands analysis of DGGE profiles. (a) Absolute values of first PLS loading, peak-picked to show bands that are most responsible for distinguishing between the groups. Greyed area indicates range of this loading across the training segments. (b) Greyscale image view of complete aligned dataset, on the same Rf axis.CC BY · PubMed Central
Figure 5 Top-ranked discriminating bands. Boxplots summarizing the normalized intensities of the four top-ranked discriminating bands, measured separately for each of the three groups.
Figure 5 Top-ranked discriminating bands. Boxplots summarizing the normalized intensities of the four top-ranked discriminating bands, measured separately for each of the three groups.CC BY · PubMed Central
Figure 6 Bacteroides specific DGGE profiles. (a) Example of DGGE profiles obtained with Bacteroides specific primes in faecal samples obtained from IBS, UC and control subjects. (b) Boxplots showing band numbers in DGGE profiles of faecal samples taken from UC, IBS, and control.
Figure 6 Bacteroides specific DGGE profiles. (a) Example of DGGE profiles obtained with Bacteroides specific primes in faecal samples obtained from IBS, UC and control subjects. (b) Boxplots showing band numbers in DGGE profiles of faecal samples taken from UC, IBS, and control.CC BY · PubMed Central

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Metadata

Authors
Noor, S. O., Ridgway, K., Scovell, L., Kemsley, E. K., Lund, E. K., Jamieson, C., Johnson, I. T., & Narbad, A.
Affiliations
  • Norwich Research Park (GB)
  • Norfolk and Norwich University Hospital (GB)
Corresponding author
Narbad, Arjan
ORCID
Venue
BMC Gastroenterology
Publisher
Springer Science and Business Media LLC
Published
2010-11-12
Volume
10
Issue
1
Pages
134-134
ISSN
1471-230X (ISSN-L)
DOI
10.1186/1471-230x-10-134
PMC
PMC3002299
OpenAlex
W2086580205
Cited by
227
References
56
Citations by year
2026: 4 · 2025: 7 · 2024: 12 · 2023: 15 · 2022: 10 · 2021: 12 · 2020: 17 · 2019: 22 · 2018: 16 · 2017: 6 · 2016: 15 · 2015: 27 · 2014: 23 · 2013: 15 · 2012: 15
FWCI
5.35
Type
journal article
Language
en
Open access
Licence
Locations
  • BMC Gastroenterology (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • UEA Digital Repository (University of East Anglia) (submittedVersion)
Funders
Biotechnology and Biological Sciences Research Council
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Health Sciences › Medicine › Gastroenterology › Inflammatory Bowel Disease
  • Health Sciences › Medicine › Gastroenterology › Gastrointestinal motility and disorders
Keywords
ulcerative colitis, irritable bowel syndrome, gut microbiota, Bacteroides, Bacteroides vulgatus, Bacteroides ovatus, Bacteroides uniformis, Parabacteroides, bacterial diversity, 16S rRNA gene sequencing, PCR-DGGE, inflammatory bowel disease, dysbiosis
MeSH terms
Adult, Bacteroides, Colitis, Ulcerative, Feces, Female, Humans, Male, Middle Aged, Multivariate Analysis, Case-Control Studies, Polymerase Chain Reaction, Gastrointestinal Tract, Irritable Bowel Syndrome, Young Adult, Denaturing Gradient Gel Electrophoresis, Molecular Typing

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