Study of the microbiota composition in adult celiac disease

• Grant: FC 016/2015
• Title: Study of the composition of the intestinal microbiota in adult coeliac disease
• Topic: Celiac Disease, Infection and Inflammation
• Duration: Biennial Project
• Principal Investigator: Prof. Rachele Ciccocioppo, Gastroenterology Unit, Department of Medicine, A.O.U.I. Borgo Roma and University of Verona
• Partnerships:Prof. Enrica Capelli, Laboratory of Immunology and Genetic Analysis, Department of Earth and Environmental Science, University of Pavia; Prof. Federico Biagi, Gastroenterology Unit, ICS Maugeri, University of Pavia; Prof. Gino Roberto Corazza, Department of Internal Medicine and Therapeutics, Fondazione I.R.C.C.S. Policlinico San Matteo and University of Pavia

Publications originating from the Project:

• Panelli S, Capelli E, Lupo GFD, et al. Comparative Study of Salivary, Duodenal, and Fecal Microbiota Composition Across Adult Celiac Disease. J Clin Med 2020;9:1109. Published 2020 Apr 13. doi:10.3390/jcm9041109 https://pubmed.ncbi.nlm.nih.gov/32294965/
• Schiepatti A, Bacchi S, Biagi F, Panelli S, Betti E, Corazza GR, Capelli E, Ciccocioppo R. Relationship between duodenal microbiota composition, clinical features at diagnosis, and persistent symptoms in adult Coeliac disease. Dig Liver Dis. 2021 Mar 16:S1590-8658(21)00088-8. doi: 10.1016/j.dld.2021.02.019. Epub ahead of print. PMID: 33741248. https://pubmed.ncbi.nlm.nih.gov/33741248/

THE STUDY

Project rationale and aims

Coeliac disease is a chronic immune-mediated enteropathy, which develops as a consequence of a complex interplay between genetic and environmental factors. In individuals carrying HLA-DQ2/DQ8 molecules, the ingestion of gluten leads to an abnormal intestinal immune response involving both the adaptive and the innate immunity and finally leading to the intestinal damage. However, the role of gluten and the HLA-DQ2/DQ8 molecules is not sufficient to fully explain the pathogenesis and the heterogeneous clinical manifestations of coeliac disease. In this regard, there is growing evidence that an altered duodenal microbiota composition (i.e., dysbiosis) may contribute to the pathogenesis and clinical picture of coeliac disease. These studies have been conducted mainly in the pediatric setting and similar studies in adults are scarce.

Research plan and results obtained

We aimed to perform a comparative analysis of the gut microbiota in adulthood coeliac disease to evaluate whether: (i) dysbiosis anticipates mucosal lesions, (ii) gluten-free diet restores eubiosis, (iii) refractory coeliac disease has a peculiar microbial signature, and (iv) salivary and fecal communities overlap the mucosal one.

A total of 52 coeliac patients were enrolled. Thirteen of them had active coeliac disease, 29 treated coeliacdisease, 4 refractory coeliac disease, and 6 potential coeliac disease. Thirty one patients affected by functional dyspepsia served as controls.

A reduction of both α- and β-diversity was found in coeliac disease. This was already evident in patients with potential coeliac disease and achieved the nadir in refractory coeliac patients. Taxonomically, mucosa displayed a significant abundance of Proteobacteria and an expansion of Neisseria, especially in active patients, while treated coeliacs showed an intermediate profile between active disease and controls. Results on the saliva community mirrored the results on mucosal samples better than stool.

Experimental design and methodologies

This is a cross-sectional study involving adult patients with different form of coeliac disease, who were prospectively enrolled in a tertiary centre. Diagnosis of the different forms of coeliac disease was made in accordance with major international guidelines. A 16S rRNA-based amplicon metagenomic approach was applied to determine the microbiota structure and composition of salivary, duodenal mucosa, and stool samples, followed by appropriate bioinformatic analyses.

Potential pitfalls and caveats

The main drawback of our work is represented by the small sample size. However, it should be pointed out that only those patients who agreed to collect all biological samples were enrolled and that potential coeliac disease and refractory coeliac disease are rare conditions. Another potential limitation is due to the fact that we enrolled as controls patients suffering from functional dyspepsia. Although dyspepsia does not represent a real control condition, a peculiar dysbiosis, largely dominated by the phylum Proteobacteria, genus Neisseria, was evident in coeliac patients, even before the development of the enteropathy. 

Conclusions and discussion

We have shown that expansion of pathobiontic species anticipates villous atrophy and achieves the maximal divergence from controls in patients affected by refractory CD. The presence of an altered microbial community not only in active coeliac disease, but also in treated coeliac patients on a long-term gluten free diet shows that gluten avoidance is not entirely able to restore a normal microbial profile. This clearly urges the need for additional non-dietary therapies in coeliac patients. The overlapping results between mucosal and salivary samples may indicate the use of saliva as a diagnostic fluid. In conclusion, our data pave the way for future studies on larger sample sizes and support the utility of gut microbiota manipulation for preventive and therapeutic purposes in adulthood CD.