Evaluation of Buccal Cell Samples for Studies of Oral Microbiota.
Author(s): Yu G, Phillips S, Gail MH, Goedert JJ, Humphrys M, Ravel J, Ren Y, Caporaso NE
Publication: Cancer Epidemiol Biomarkers Prev, 2017, Vol. 26, Page 249-253
PubMed ID: 27770008 PubMed Review Paper? No
Purpose of Paper
This paper compared the collection of buccal cell specimens using a swishing method to the collection of saliva and oral swab specimens from multiple locations on oral microbial profiles.
Conclusion of Paper
Sequencing (>1,000 reads per sample) was successful for buccal cell, buccal mucosa swab samples, and palatine tonsil swab samples from all 41 participants, for the hard palates swabs of 37 of the 41 participants, saliva of 33 participants, keratinized gingiva and tongue dorsum from 29 participants, supra-gingival plaque of 23 participants, and from sub-gingival dental plaque specimens for only 10 of the 41 participants. Buccal cell specimens had significantly more observed species, higher alpha diversity, and less beta diversity than saliva specimens and oral swabs specimens from the other seven sample sites. There were no differences in oral microbiome metrics based on age, race, sex, or smoking status.
Studies
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Study Purpose
This study compared the collection of buccal cell specimens using a swishing method to the collection of saliva and oral swab specimens from several locations on alpha diversity and beta diversity (intra-participant variation) of oral microbial profiles. Eight samples were collected from individuals with no antibiotic usage or professional dental cleaning within the previous 3 months or diagnosis with severe periodontal disease or cancer (25-66 years old; 20 African-Americans and 21 Caucasians; 22 males, 19 females; 22 current smokers, 19 non-smokers). Oral samples were collected by following the protocols of the Human Microbiome Project and included 2 dental plaque samples (supra- and sub-gingival plaque), saliva, and swabs from 5 soft tissue sites (keratinized gingiva, hard palate, buccal mucosa, palatine tonsil, and tongue dorsum). Oral samples were stored frozen until processing (details not provided). Buccal cells from mouthwash were collected using the protocol in the Prostate, Lung, Colorectal and Ovarian (PLCO) cancer cohort (swishing mouthwash vigorously for 45 seconds followed by expectoration) and stored refrigerated if not processed within 12 h of collection. DNA was extracted using the QIAamp DNA Mini Kit and microbiota profiles were determined by next-generation sequencing of the 16S rRNA gene V3–V4 region.
Summary of Findings:
Sequencing (>1,000 reads per sample) was successful for buccal cell, buccal mucosa swab samples, and palatine tonsil swab samples from all 41 participants, for the hard palates swabs of 37 of the 41 participants, saliva of 33 participants, keratinized gingiva and tongue dorsum from 29 participants, supra-gingival plaque of 23 participants, and from sub-gingival dental plaque specimens for only 10 of the 41 participants. Buccal cell specimens had significantly more observed species (P<0.002 for all), higher alpha diversity (P<0.05), and less beta diversity (P<0.05 all) than saliva specimens and oral swabs specimens from the seven sample sites. There were no differences in oral microbiome metrics based on age, race, sex, or smoking status.
Biospecimens
Preservative Types
- Frozen
- None (Fresh)
Diagnoses:
- Normal
Platform:
Analyte Technology Platform DNA Next generation sequencing Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Preaquisition Patient race African-American
Caucasian
Preaquisition Patient gender Female
Male
Preaquisition Patient age 25-66 years old
Preaquisition Diagnosis/ patient condition Smoker
Non-smoker
Biospecimen Acquisition Biospecimen location Supra-gingival plaque
Sub-gingival plaque
Hard palate
Saliva
Keratinized gingiva
Buccal mucosa
Buccal cells
Palatine tonsil
Tongue dorsum
Biospecimen Acquisition Method of cell acquisition Swishing
Swabbing
Biospecimen Acquisition Method of fluid acquisition Expectoration