H. pylori-infected stomach in asymptomatic individuals

Helicobacter pylori colonization of the gastric niche can persist for years in asymptomatic individuals. Although latent H. pylori infection can progress to cancer, a detailed survey of the microbiome and immune composition in the chronically infected stomach is still lacking. We collected human gastric tissues and performed metagenomic, single-cell RNA sequencing (scRNA-seq), flow cytometry and fluorescent microscopy to deeply characterize the host-microbiota environment in H. pylori-infected (HPI) stomachs. HPI asymptomatic individuals showed dramatic changes in the composition of gastric microbiome and immune cells compared to non-infected individuals. With metagenomic data, we also demonstrated antibiotic resistant genes, enzymes and pathways alteration related to metabolism and immune response. scRNA-seq and flow cytometry data revealed that in contrast to murine stomachs, ILC2 are virtually absent in the human gastric mucosa, whereas ILC3 are the dominant population in healthy and asymptomatic HPI individuals. Specifically, NKp44+ ILC3s were highly increased in the gastric mucosa of asymptomatic HPI individuals, and their proportions correlated with the abundance of selected microbial taxa found to be enriched in the infected mucosa. In addition, CD11c+ myeloid cells, activated CD4 T cells and B cells were expanded in HPI individuals. In HPI individuals, B cells acquired an activated phenotype and progressed into a highly proliferating germinal center stage and plasmablast maturation, which correlated with the presence of tertiary lymphoid structures within the gastric lamina propria. Our study provides a comprehensive atlas of the gastric mucosa-associated microbiome and immune cell landscape from asymptomatic HPI as compared to uninfected individuals. Library details : More in detail, material from uninfected antrum samples was pooled, as was the material from uninfected fundus samples, HPI antrum samples and HPI fundus samples. After cell hashing of fundus/antrum and sorting of the populations of interest, samples were further pooled (HPI antrum with HPI fundus, control antrum with control fundus) into 4 samples to be processed in 4 separate wells of a 10X chip. We then obtained gene expression libraries and hashtag libraries from each sample, for a total of 8 libraries: a1 (gene expression library for pooled ILC & myeloid cells from uninfected individuals); a2 (gene expression library for pooled ILC & myeloid cells from HPI indivuduals ); a3 (gene expression library for pooled Lineage+ / T cells from uninfected individuals ); a4 (gene expression library for pooled Lineage+ / T cells from HPI indivuduals ); a5, a6, a7 and a8 are the hashtag libraries corresponding to a1, a2, a3 and a4 respectively. Sequencing data were obtained from 4 flow cells/library (only 3 flow cells for library a1), hence the total number of 31 files in the ENA entry.