Gastric Helicobacter pylori infection perturbs human oral microbiota

Abstract

Background: We investigated the effects of gastric Helicobacter pylori infection on the daytime and overnight human oral microbiota.

Methods: Twenty four volunteers were recruited. Ten tested positive for H. pylori infection by the Carbon-14 Urea Breath Test, and the rest were negative. Two oral swabs were collected: one immediately after waking up in the morning and before brushing teeth, and another in the evening before teeth-brushing. DNA extract acquired from each swab was subjected to Illumina sequencing of 16S rRNA gene amplicons. The microbial abundance and composition were analysed in relation to H. pylori infection status.

Results: Helicobacter pylori-positive individuals had significant changes in the alpha and beta diversities in the daytime samples in comparison to those who were H. pylori negative. To identify which taxa could be significantly affected within the cohorts in the daytime, we employed the LEfSe method. When compared against UBT-negative samples, significantly higher abundances were detected in both Pseudomonas and Roseomonas, while Fusobacterium, Solobacterium, Haemophilus and Streptococcus were significantly decreased in the UBT-positive samples.

Discussion: Our data demonstrated that H. pylori infection affects the human daytime oral microbiota. The hitherto undocumented changes of several bacterial genera due to H. pylori infection require more studies to examine their potential health effects on affected individuals.

Keywords: 16S rRNA sequencing; Helicobacter pylori; Metagenomics; Oral microbiome; Urea breath test.

Figure 1. Core bacterial genera identified among the daytime and overnight samples.

A minimum threshold of 0.9 was employed for the identification of core genera among the daytime and overnight samples.

Figure 2. Rarefaction curve plots of the daytime and overnight samples.

(A) Rarefaction curve of daytime samples based on the numbers of observed species. (B) Rarefaction curve of overnight samples based on the numbers of observed species. (C) Rarefaction curve of daytime samples based on Shannon diversity index. (D) Rarefaction curve of overnight samples based on Shannon diversity index.

Figure 3. Daytime comparison of microbial diversity between the UBT-negative and UBT-positive cohorts.

Boxplot of Shannon index depicts significant differences in daytime bacterial diversity between the UBT-negative and UBT-positive cohorts.

Figure 4. PCoA plot based on weighted UniFrac distance metric comparing overnight OTU abundances between UBT-positive and UBT-negative cohorts.

Figure 5. PCoA plot based on weighted UniFrac distance metric comparing daytime OTU abundances between UBT-positive and UBT-negative cohorts.

Figure 6. Identification of bacterial phyla and genera with significant differences between the UBT-negative and UBT-positive daytime samples using LEfSe analysis.

(A) Significantly differentially abundant bacterial phyla identified by LEfSe analysis. (B) Significantly differentially abundant bacterial genera identified by LEfSe analysis.