Archives of oral biology · 2026
Oral microbiome profiles in a RUT-confirmed gastric H. pylori-positive cohort: A retrospective pilot comparison of specimen-processing workflows.
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Méndez Javiera Ortiz, Canedo-Marroquín Gisela, Brinkac Leone Lauren, Greco Chris, Nelson Karen, Inostroza Silva Carolina
Аннотация
OBJECTIVE: To characterize oral microbial profiles in a rapid urease test (RUT)-confirmed gastric Helicobacter pylori-positive cohort and descriptively compare oral specimen-processing workflows.
DESIGN: Archived oral specimens collected during 2015-2016 from adults undergoing diagnostic upper gastrointestinal endoscopy were retrospectively analyzed. Gastric H. pylori status was confirmed by RUT of antral biopsies. The microbiome dataset comprised 32 DNA preparations from 18 RUT-positive participants: 11 buccal-NucleoSpin, 11 saliva-NucleoSpin, and 10 saliva-PowerSoil preparations. Buccal- and saliva-NucleoSpin samples were paired in 11 participants; three also contributed saliva-PowerSoil preparations. The V4 region of the 16S rRNA gene was sequenced using Illumina MiSeq. Alpha diversity, Bray-Curtis dissimilarity, and taxonomic relative abundances were evaluated using the historical workflow.
RESULTS: Buccal-NucleoSpin and saliva-NucleoSpin preparations showed comparable alpha diversity. Shannon diversity did not differ between buccal and saliva specimens (p = 0.13), including when restricted to paired participants. Historical Bray-Curtis comparisons showed differences between buccal and saliva-derived profiles (p = 0.00572); however, the original multivariate model, permutation structure, effect sizes, and dispersion testing could not be retrospectively verified. Taxonomic findings were therefore interpreted descriptively. Saliva-NucleoSpin profiles showed higher relative representation of Streptococcus and Veillonella, whereas buccal-NucleoSpin profiles showed higher relative representation of Neisseria and Pseudomonas. No Helicobacteriaceae signal remained after filtering.
CONCLUSIONS: Oral microbiome profiles differed among specimen-processing workflows. Buccal-swab and saliva-derived preparations provided complementary representations; however, because specimen type, preservation, and extraction procedures were not fully crossed, their individual contributions could not be separated. Standardized sampling and laboratory procedures are essential for reproducible oral microbiome studies.
DESIGN: Archived oral specimens collected during 2015-2016 from adults undergoing diagnostic upper gastrointestinal endoscopy were retrospectively analyzed. Gastric H. pylori status was confirmed by RUT of antral biopsies. The microbiome dataset comprised 32 DNA preparations from 18 RUT-positive participants: 11 buccal-NucleoSpin, 11 saliva-NucleoSpin, and 10 saliva-PowerSoil preparations. Buccal- and saliva-NucleoSpin samples were paired in 11 participants; three also contributed saliva-PowerSoil preparations. The V4 region of the 16S rRNA gene was sequenced using Illumina MiSeq. Alpha diversity, Bray-Curtis dissimilarity, and taxonomic relative abundances were evaluated using the historical workflow.
RESULTS: Buccal-NucleoSpin and saliva-NucleoSpin preparations showed comparable alpha diversity. Shannon diversity did not differ between buccal and saliva specimens (p = 0.13), including when restricted to paired participants. Historical Bray-Curtis comparisons showed differences between buccal and saliva-derived profiles (p = 0.00572); however, the original multivariate model, permutation structure, effect sizes, and dispersion testing could not be retrospectively verified. Taxonomic findings were therefore interpreted descriptively. Saliva-NucleoSpin profiles showed higher relative representation of Streptococcus and Veillonella, whereas buccal-NucleoSpin profiles showed higher relative representation of Neisseria and Pseudomonas. No Helicobacteriaceae signal remained after filtering.
CONCLUSIONS: Oral microbiome profiles differed among specimen-processing workflows. Buccal-swab and saliva-derived preparations provided complementary representations; however, because specimen type, preservation, and extraction procedures were not fully crossed, their individual contributions could not be separated. Standardized sampling and laboratory procedures are essential for reproducible oral microbiome studies.