Investigation of duodenal microbiota in celiac diagnosed patients following gluten-FREE diet by next generation sequencing method

Objective: Celiac disease (CD) is a chronic inflammatory disease of the small intestine characterized by a persistent intolerance to dietary gluten. The only known treatment for celiac disease is gluten-free diet therapy. Today, it has been shown in the literature that dietary components affect the gut microbiota. In this study, it was aimed to identify the specific composition of the regenerated duodenal microbiota in asymptomatic celiac patients following a gluten-free diet after active disease state by next-generation sequencing method and to analyze the data by literature-based comparison. Method: Endoscopy was performed for duodenum biopsy and biopsy samples were taken from 10 celiac patients who were on a gluten-free diet. Collected biopsies were stored at -20°C until sequencing after DNA extraction. Sequencing was performed on the Illumina NextSeq 550 next generation sequencing platform and duodenal microbiota composition was analyzed. Results: Five men and five women were included in the study and their average age was 38.1. A total of 36 different bacterial phyla were detected in the samples. The most common phyla were 31.46% Firmicutes, 21.47% Proteobacteria, 10.6% Bacteroidetes and 6.1% Actinobacteria. When analyzing the samples as families, it is seen that Bacillaceae 1 (3.35%) and Streptococcaceae (2.94%) groups are the two families with the highest abundance. At the genus level, Streptococcus (1.44%) and Geobacillus (1.31%) species have the highest percentage among samples. The average number of species of the samples was calculated as 232.2. According to Shannon index, diversity was found lower in the three samples that were grouped differently in PCoA compared to the other samples. Conclusion: In this study, Firmicutes was the most common phylum in celiac patients on a gluten-free diet. Firmicutes was the dominant phylum in 7 of the samples, while Proteobacteria was dominant in 3 of the samples. In PCoA and Hierarchical cluster tree, 7 patients showed similar profiles, while 3 patients had a different duodenal flora. Keywords: celiac disease, duodenal microbiota, next-generation sequencing, 16s rRNA