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Differential clustering of faecal and mucosa-associated microbiota in healthy individuals
Örebro University, School of Medical Sciences. Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden; Department of Internal Medicine, Ersta hospital, Stockholm, Sweden.
Department of Microbiology, Tumor and Cell biology & Science for Life Laboratory, Karolinska Institute, Solna, Sweden.
Department of Microbiology, Tumor and Cell biology & Science for Life Laboratory, Karolinska Institute, Solna, Sweden; Division for Family Medicine, Karolinska Institute, Stockholm, Sweden; Stress Research Institute, Stockholm University, Stockholm, Sweden.
Clinical Epidemiology and Biostatistics, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
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2018 (English)In: Journal of Digestive Diseases, ISSN 1751-2972, E-ISSN 1751-2980, Vol. 19, no 12, p. 745-752Article in journal (Refereed) Published
Abstract [en]

BACKGROUND: Faecal samples are often used to characterise gut microbiota, since they are easily collected. However, whether or not the faecal microbiota differ from the mucosa-associated microbiota remains largely unknown. This may be specifically relevant in conditions that are characterised by complex mucosal microbe-host interactions, such as Crohn's disease. We aimed to determine the degree of agreement between faecal and mucosal microbiota profiles in healthy individuals, using two commonly used collection procedures.

MATERIAL AND METHODS: The gut microbiota composition of faecal samples (sent at ambient temperature before storage at -70°C) and of colonic biopsies (obtained at endoscopy and immediately stored at -70°C) was determined by sequencing the 16S rRNA gene. Thirty-one randomly selected healthy individuals from the population-based colonoscopy (Popcol) study were included.

RESULTS: Faecal samples were characterised by a reduced degree of richness (p<0.0001) and diversity (p=0.016), and also differences in several phyla, including a lower relative abundance of Proteobacteria (p<0.0001) and Verrucomicrobia (p=0.008) than in biopsies. Only 3 of 30 individuals had a similar faecal and mucosal microbiota profile, based on weighted UniFrac analysis. A difference in Crohn's disease dysbiosis-associated bacteria was observed, including a lower relative abundance of Faecalibacterium (p=0.004) and a higher relative abundance of Ruminococcus (p=0.001) in faeces than in biopsies.

CONCLUSIONS: Analysis of faecal samples that have been transported at ambient temperature does not adequately reflect the colonic mucosa-associated microbiota in healthy individuals. These findings have implications for the interpretation of the previous literature, and may be specifically relevant to studies on Crohn's disease.

Place, publisher, year, edition, pages
Wiley-Blackwell Publishing Asia , 2018. Vol. 19, no 12, p. 745-752
Keywords [en]
Crohn disease, fecal microbiota, mucosa-associated microbiota
National Category
Microbiology in the medical area Gastroenterology and Hepatology
Identifiers
URN: urn:nbn:se:oru:diva-70345DOI: 10.1111/1751-2980.12688ISI: 000455494100004PubMedID: 30467977Scopus ID: 2-s2.0-85059893806OAI: oai:DiVA.org:oru-70345DiVA, id: diva2:1266045
Funder
Swedish Research Council, 2012-1930 2011-2764
Note

Funding Agencies:

Örebro University  

Bengt Ihre Foundation  

Nanna Svartz Foundation  

Örebro University Hospital Research Foundation  

Örebro County Research Foundation  

Söderberg Foundation  

Swedish Foundation for Gastrointestinal Research 

Available from: 2018-11-27 Created: 2018-11-27 Last updated: 2021-09-20Bibliographically approved
In thesis
1. Chronic inflammatory bowel diseases: studies of microbiota and its influence
Open this publication in new window or tab >>Chronic inflammatory bowel diseases: studies of microbiota and its influence
2021 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Introduction: Inflammatory bowel diseases are becoming increasingly common. The underlying mechanisms are not entirely known but the gut microbiota seem to be involved in the pathogenesis. 

Aim: The aim of this thesis was to characterise gut microbiota related to diagnosis, disease course and response to biological treatment, taking aspects of the source of biological material into account. 

Materials and methods: Patients and healthy individuals from several different cohorts in Sweden and Europe were invited. Faecal samples and mucosal biopsies were analysed using different sequencing platforms to investigate the gut microbiota. In Study I the faecal microbiota was correlated to different inflammatory bowel diseases. In Study II we compared the microbiota in faeces to the microbiota in mucosal biopsies. In StudyIII we related the faecal microbiota to the outcome of biological treatment. In Study IV we investigated the diagnostic and prognostic properties of the GAmapTM Dysbiosis Test.

Results: The faecal microbiota in collagenous colitis resembles the faecalmicrobiota in inflammatory bowel disease. The faecal microbiota differs from the mucosal microbiota. Faecal microbiota at initiation of biological treatment among patients with Crohn’s disease differ between responders and non-responders. The GAmapTM Dysbiosis Test discriminates patients with inflammatory bowel disease from healthy individuals.

Conclusion: Collagenous colitis may share microbial underpinnings with other inflammatory bowel diseases. Conclusions about mucosal interactions with the gut microbiota should be made with caution when usingfaecal samples to characterise the microbiota. In Crohn’s disease, the faecal microbiota may be included in a model to predict the outcome of biological treatment. The GAmap Dysbiosis Test does not seem to be superior to other current diagnostic tools in clinical decision-making. 

Place, publisher, year, edition, pages
Örebro: Örebro University, 2021. p. 133
Series
Örebro Studies in Medicine, ISSN 1652-4063 ; 248
Keywords
Inflammatory bowel disease, microscopic colitis, Crohn’s disease, ulcerative colitis, microbiota, microbiome, biological treatment
National Category
General Practice
Identifiers
urn:nbn:se:oru:diva-93138 (URN)9789175294049 (ISBN)
Public defence
2021-10-14, Örebro universitet, Campus USÖ, hörsal C1, Södra Grev Rosengatan 32, Örebro, 09:00 (Swedish)
Opponent
Supervisors
Available from: 2021-07-26 Created: 2021-07-26 Last updated: 2021-10-22Bibliographically approved

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Carstens, AdamHalfvarson, Jonas

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