() related chronic gastritis is a well-known major etiological factor for gastric cancer development. However, -negative gastritis (HpN) is not well described. We aimed to examine gastric mucosal microbiota in HpN compared to -positive gastritis (HpP) and -negative non-gastritis group (control). Here, we studied 11 subjects with HpN, 40 with HpP and 24 controls. We performed endoscopy with six gastric biopsies. Comparison groups were defined based on strict histological criteria for the disease and diagnosis. We used 16S rRNA gene amplicon sequencing to profile the gastric microbiota according to comparison groups. These results demonstrate that the HpP group had significantly lower bacterial richness by the operational taxonomic unit (OTU) counts, and Shannon and Simpson indices as compared to HpN or controls. The linear discriminant analysis effect size analysis showed the enrichment of Firmicutes, Fusobacteria, Bacteroidetes and Actinobacteria at phylum level in the HpN group. In the age-adjusted multivariate analysis, sp. and were at a significantly increased risk for HpN (odds ratio 18.9 and 12.3, respectively) based on abundance. sp. was uniquely found in HpN based on occurrence. In this paper, we conclude that sp., and sp. are candidate pathogenic bacterial species for HpN. These results if confirmed may have important clinical implications.