Study design
An observational study was conducted between September 2014 and May 2016. The study population comprised patients who presented with gastric symptoms and were diagnosed with H. pylori infection based on positive rapid urease tests conducted on gastric biopsy specimens. The inclusion criteria were as follows: 20 years or older, having own teeth, and no oral symptoms that require immediate treatment. Those with drug allergies and pregnant women were excluded. Twelve patients were analyzed (Additional file 1; Table S1). They were prescribed a 1-week course of a triple-drug regimen (30 mg lansoprazole, 750 mg amoxicillin, and 200 mg clarithromycin, twice daily) as the primary eradication regimen. In cases in which the primary treatment failed, 250 mg metronidazole was used instead of clarithromycin as the secondary regimen.
Clinical examinations
Oral malodor and oral clinical symptoms were evaluated on the date of initiation of H. pylori eradication treatment and 1 and 7 weeks thereafter. The severity of oral malodor was determined by OLT [13] and GC. A gas chromatograph (GC2014; Shimadzu, Kyoto, Japan) was used to assay the concentrations of H2S, CH3SH, and CH3SCH3 in mouth air. The average probing pocket depth (PPD), the percentage of bleeding on probing (BOP) values, the plaque index (PlI) [17], and the tongue coating score (TCS) [14] were evaluated. The ammonia concentration was measured using a portable ammonia-monitoring device (ATTAIN; Taiyo, Osaka, Japan). Saliva samples were obtained by stimulation using chewing gum (CheckBuf; Morita, Osaka, Japan) and subjected to sequencing of the 16S rRNA gene amplicons and quantitative analysis of bacterial species. These examinations were conducted at 9 am; the subjects were prohibited from eating, drinking, chewing, smoking, brushing teeth, or rinsing their mouth after waking up.
Quantitative analysis of bacterial species in saliva
Quantitative analysis of 12 bacterial species and all bacteria in saliva was performed using the fibrous DNA chip Genopal® (Mitsubishi Chemical, Tokyo, Japan). The bacterial species were classified into the red (Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola), orange (Campylobacter rectus, Fusobacterium nucleatum, Prevotella intermedia, and Prevotella nigrescens), green (Aggregatibacter actinomycetemcomitans and Capnocytophaga gingivalis), and yellow (Streptococcus gordonii, Streptococcus intermedius, and Streptococcus mutans) groups [18], and the proportions of these groups among the total oral bacteria were evaluated.
Sequencing of 16S rRNA gene amplicons
DNA was extracted from each saliva sample [19] and the V1-V2 regions of the 16S rRNA gene were amplified by PCR using the universal bacterial primers 8F and 338R with adaptor and sample-specific 8-base tag sequences [20]. Following emulsion PCR, sequencing was performed on the Ion PGM using an Ion PGM Hi-Q View sequencing kit (Thermo Fisher Scientific, Waltham, MA). The raw sequencing reads were quality-filtered [21]. The quality-checked reads were assigned to the appropriate sample by examining the tag sequence. Similar sequences were assigned to operational taxonomic units (OTUs) using UPARSE [22], with a minimum pairwise identity of 97%. The taxonomy of each representative sequence was determined using blast against oral bacterial 16S rRNA gene sequences in the Human Oral Microbiome Database [23]. Nearest-neighbor species with ≥98.5% identity were selected as candidates for each OTU. The taxonomy of an OTU without any hits was determined to the genus level using the Ribosomal Database Project classifier with a minimum support threshold of 80%. The alpha diversity index and UniFrac distances [24] were calculated following rarefaction to 5,000 reads per sample.
Statistical analysis
The Wilcoxon signed-rank test was used to compare malodor, clinical, and bacterial parameters among baseline, 1 week, and 7 weeks. The relative abundance of bacterial genera after 1 and 7 weeks were compared with those at baseline using Dunnett’s test. Statistical analyses were conducted using R software, version 3.6.1 [25].