Celiac disease and the gastrointestinal microbiome - comparison of bacterial profiles associated with the gastric and duodenal mucosa in children with newly diagnosed celiac disease and controls using next-generation sequencing (NGS)

Dominika Salamon1*, Kinga Kowalska-Duplaga2, Agnieszka Krawczyk1, Agnieszka Sroka-Oleksiak1, Tomasz Gosiewski1

1 Department of Molecular Medical Microbiology, Department of Microbiology, Faculty of Medicine Jagiellonian University.
Jagiellonian University Collegium Medicum, Poland
2 Department of Pediatrics, Gastroenterology and Nutrition, Faculty of Medicine Jagiellonian University Collegium Medicum, Poland
*E-mail: dominika.salamon@uj.edu.pl

Celiac disease (celiac disease-CD) is a multi-organ autoimmune disease associated with an abnormal reaction to gluten (a fraction of cereal proteins). A gluten-containing diet damages the mucosa of the small intestine in genetically predisposed individuals, leading to malabsorption of inediencies. Numerous studies on CD also include analysis of the gastrointestinal microbiome, but most often focus on the lower gastrointestinal tract (stool samples). The aim of the current study was to evaluate the upper gastrointestinal (GOPP) microbiome in children with newly diagnosed celiac disease. Biopsy specimens from the stomach and duodenum were collected in 2019-2021 from 73 children and adolescents aged 2-18 years assigned to one of two groups: 1) 60 patients with newly diagnosed CD based on clinical symptoms, immunologic findings and histopathologic results of biopsy specimens; 2) 13 children without GOPP inflammatory disease - the control group. The GOPP microbiome was assessed by sequencing the V3 and V4 regions of the bacterial 16S rRNA subunit using NGS (Next-generation Sequencing) on a MiSeq sequencer (Illumina). The minimum/maximum number of reads was 16729/139310, and the number of species was 215/623. Detailed taxonomic analyses were performed at the L2 (type) and L7 (species) levels separately for duodenal and gastric samples. At the L2 level, significantly more Proteobacteria were found in the control group, both in the duodenum (p=0.02) and stomach (p=0.01). At the L7 level, significant differences (p<0.005) were found in the duodenum for 9 species (including Pseudomonas plecoglossicida), and in the stomach for 8 (including Bifidobacterium bifidum). There were no significant differences between CD and control for alpha diversity indices (Chao1; Shannon; Simpson), except for duodenal samples at L7 for the Chao1 index (p=0.04). For beta diversity, no significant differences were found between CD and controls (BaryCurtis, Jaccard, Jensen - Shannon indices). The NGS study of the GOPP microbiome was performed separately for the duodenum and stomach, which is new for this type of study. A difference in the taxonomic composition of the microbiome was demonstrated for the duodenum at the species level (L7) and only for one indicator - further analysis at other levels is needed.

Source of funding: SONATA Bis (NCN grant), No. 2017/26/E/NZ5/00266.

The presented work is an independent study by its authors.