The Microbiota of Gastric Premalignant Lesions: 16S Sequencing Data in a Central American Population

Abstract

Introduction: Gastric cancer develops through a cascade, from gastritis to atrophic gastritis and gastric intestinal metaplasia, to dysplasia and adenocarcinoma. Helicobacter pylori (Hp) plays a prominent role in this cascade, contributing to the high cancer incidence in regions such as Central America, but the role of other bacteria is less defined. We compared the gastric microbiota of patients with and without premalignant lesions (atrophic gastritis or intestinal metaplasia). Methods: We sequenced the V3—V4 region of the 16S ribosomal RNA gene extracted from gastric corpus biopsies obtained during routine clinical endoscopies at the national university hospital in Leon, Nicaragua. Using the Illumina MiSeq platform and QIIME processing pipeline, we obtained microbiota measures of alpha diversity, beta diversity, and individual taxa-both phyla and operational taxonomic units (OTUs). We compared these measures between groups using the Kruskal—Wallis test. Results: Of 81 subjects, 30 had premalignant lesions and 51 did not, with characteristics described in Table 1. Firmicutes was the dominant phylum in both groups, but only composed 43% of sequences in the premalignant group, compared to 68% of non—premalignant sequences (Figure 1). The difference was related to the Proteobacteria phylum (35% of OTUs in premalignant and 18% in non—premaligant), predominantly from Hp. No differences in alpha or beta diversity existed between groups however, whether calculated with Hp reads included or excluded (Figure 2). Alpha diversity was correlated with number of Hp counts (p<0.001). One OTU was found to be significantly less prevalent in premalignant than non—premalignant samples. The OTU belonged to the Bacillales order of the Firmicutes phylum (p=0.006).1216_A Figure 1 No Caption available.1216_B Figure 2. Summary of phyla detected in gastric biopsy specimens with gastric intestinal metaplasia (GIM), multifocal atrophic gastritis (MAG), non—atrophic gastritis (NAG), and “normal” histology, with H. pylori OTUs included.Conclusion: In this study of the gastric corpus microbiome, premalignant lesions were associated with increasing Hp density and a corresponding decrease in Firmicutes, but otherwise limited differences in microbiota compared to stomachs with minimal or non—atrophic gastritis on histology. Additional areas warranting study include the antrum microbiome and the microbiome in higher risk premalignant lesions (e.g., incomplete gastric intestinal metaplasia or dysplasia).1216_C Figure 3. Box plots of mean alpha diversity of corpus biopsies with and without premalignant lesions (gastric intestinal metaplasia or multifocal atrophic gastritis), according to A) Observed OTUs, B) chao1 index, C) phylogenetic diversity, D) Shannon index. Helicobacter pylori reads are excluded. No significant difference between—group difference was detected for any measure.