The gastric microbiota in patients with Crohn's disease; a preliminary study

Background. Gut dysbiosis is documented widely; however, the gastric microbiota in patients with Crohn's disease (CD) has not been studied.Aim. To evaluate differences in the composition of the human stomach microbiota between CD patients and control subjects.Methods. DNA was extracted from mucosal biopsies of the gastric corpus and antrum, and from gastric fluid samples, taken from the 24 consecutive CD patients and 19 control individuals. Samples were PCR-amplified and subjected to 16S rRNA gene sequencing.Results. Sequencing identified 1511 operational taxonomic units (OTUs), of which 239 passed the low abundance and low variance filters. All but one CD patients and 13 controls were HPnegative. Fifteen bacterial phyla were identified in at least one gastric mucosal or gastric fluid site in HP-negative individuals. Of these, Bacteroidota and Proteobacteria accounted for 70% of all phyla, and Firmicutes, Actinobacteriota, and Fusobacteriota combined accounted for 27%. There was significant difference in the relative abundance of Bacteroidota, Proteobacteria, Fusobacteriota, and Campilobacterota between CD patients and control subjects only in gastric corpus samples. In gastric liquid samples, there was a significant difference only in Actinobacteriota. Pairwise comparison identified 67 differentially abundant OTUs in at least one site. Of these, 13 were present in more than one comparison, and four differentiating OTUs (Neisseriaceae, Neisseria, Absconditabacteriales, and Microbacteriaceae) were identified at all tested sites.Conclusion: The results reveal significant changes in microbial profiles (beta diversity, phylum, and individual taxa levels) of gastric mucosal and fluid samples between H. pylori-negative CD patients and control subjects.