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The gut-adherent microbiota of PSC–IBD is distinct to that of IBD
  1. Mohammed Nabil Quraishi1,
  2. Martin Sergeant2,
  3. Gemma Kay2,
  4. Tariq Iqbal3,
  5. Jacqueline Chan2,
  6. Chrystala Constantinidou2,
  7. Palak Trivedi1,
  8. James Ferguson1,
  9. David H Adams1,
  10. Mark Pallen2,
  11. Gideon M Hirschfield1
  1. 1 National Institute for Health Research (NIHR) Birmingham, Liver Biomedical Research Unit, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
  2. 2 Department of Microbiology and Infection, University of Warwick, Warwick, UK
  3. 3 Department of Gastroenterology, Queen Elizabeth Hospital Birmingham, Birmingham, UK
  1. Correspondence to Dr G M Hirschfield, Centre for Liver Research, Institute of Immunology and Immunotherapy, Wolfson Drive, University of Birmingham, Birmingham, B15 2TT, UK; g.hirschfield{at}

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Primary sclerosing cholangitis–IBD (PSC–IBD) is an inflammatory autoimmune hepato–biliary–enteric disease in which it is predicted that gut microbiota have potential pathophysiological effects, relevant to disease initiation and outcome. The recent article by Kummen et al 1 who reported that the gut microbiota in PSC is distinct compared with those from healthy controls and patients with UC without liver disease, is therefore of interest. However, it remains unclear if these alterations in the gut microbiota are a cause or an effect of liver disease, and there remains a challenging task to link dysbiosis with disease pathogenesis, as well as clarify whether faecal microbiota are entirely representative of communities of mucosa-associated bacteria, which might uniquely interact with immune and epithelial cells.

Nevertheless Kummen et al notably demonstrated that the Veillonella genus showed a marked increase in PSC–IBD, in comparison with both healthy controls and patients with UC alone. Given interest in the mechanism of lymphocyte tracking between the bowel and liver in PSC–IBD and, in particular, the role of vascular adhesion protein-1 (VAP-1), a potent semicarbazide-sensitive amine oxidase and adhesion molecule, critical for effector cell recruitment to the liver, it is relevant to note that Veillonella species contain genes encoding copper amine oxidase proteins.2 ,3

In order to characterise mucosa-adherent bacteria in PSC–IBD patients further, we performed 16s-rRNA analysis of colonic tissue from the ascending, transverse and descending colon in patients undergoing colonoscopy with IBD alone (N=10), PSC–IBD (N=11) and healthy controls (N=9). DNA was extracted from the biopsy samples using FASTSpin Kit and gut microbiota was characterised using 16 s rRNA-based analysis of the V3–V4 region on the Illumina MiSeq. The reads were clustered into operational taxonomic units using UPARSE and analysed using Qiime and the Vegan package in R. Parallel to the study by Kummen et al, we found that patients with PSC–IBD have a distinct mucosally adherent gut microbiota compared with those with IBD alone and healthy controls (figure 1; p=0.001). We demonstrated significant increases in Escherichia, Lachnospiraceae and Megasphera in the patients with PSC–IBD compared with controls. Similar to the Veillonella genus reported by Kummen et al, these bacteria have genes that encode for amine oxidases and are all potent producers of primary amines that could act as VAP-1 substrates.4 We also demonstrated that patients with PSC had a reduced abundance of Prevotella and Roseburia (butyrate producer) and a near-absence of Bacteroides. Butyrate is a short chain fatty acid that enhances intestinal barrier function by facilitating intracellular tight junction assembly and lower butyrate may contribute to a loss of barrier integrity and dysregulated mucosal immunity. The microbiota did not differ significantly based on the site of biopsy in the three groups of patients.

Figure 1

16 s rRNA-based analysis (Illumina MiSeq) of mucosa-associated bacteria in patients with primary sclerosing cholangitis-IBD (PSC–IBD), PSC and healthy controls undergoing elective colonoscopy was performed. A principal component analysis is shown with visualisation of observed bacterial communities based on the presence and absence of operational taxonomic units identified in PSC–IBD (blue), IBD (orange) and healthy controls (green). Analysis by UPARSE ( and the ‘Vegan’ statistical computational package demonstrates a significant difference between these disease groups (p=0.001).

Our findings therefore complement those of Kummen et al (table 1) and collectively support the hypothesis that one consequence of dysbiosis may be an associated dysregulation of mucosal immunity by modulating the aberrant homing of gut-specific lymphocytes and intestinal permeability. Resolving the relevance of the gut microbiota in PSC-IBD pathophysiology and treatment will require large-scale prospective studies across centres, with matching analytic approaches, and appropriate control for the stage of liver disease, as well as treatment by antibiotics. Additionally, the impact of microbiota manipulation by antibiotics and/or faecal microbial transplantation appears now to be justified, as part of broader efforts proposed to treat PSC–IBD.

Table 1

Summary of key studies analysing PSC microbiota


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  • Contributors MNQ, THI, DHA, MP and GMH initiated and planned the study. MNQ, MS, GK, JC, CC contributed to collection of samples, laboratory preparations and post-sequencing data processing. MS and GK performed the statistical analyses and interpreted the data. MNQ wrote the first draft of the letter; GMH revised it to the point of submission. All authors contributed to reviewing and approving the final submission. GMH is the guarantor of the study.

  • Funding MNQ, PJT, DHA and GMH are supported by the NIHR Birmingham Liver Biomedical Research Unit. This article presents independent research funded by NIHR.

  • Disclaimer The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health.

  • Competing interests None declared.

  • Ethics approval Samples were collected by the Human Biomaterials Resource Centre (HBRC). This is a Human Tissue Authority (HTA) licensed human sample biorepository (HTA research licence 12358).

  • Provenance and peer review Not commissioned; internally peer reviewed.

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