Oral microbiome in a general population - The influence of sample site and sampling method

Abstract

Oral microbiome profiles reflect the sample types and methodology used to investigate them. The composition of microbes in the oral cavity is site specific. It can also vary due to differences in how a site is sampled. Both saliva and gingiva samples were collected from participants of the RHINESSA study in Bergen in 2014-2015 (baseline). Saliva samples were also collected from the same participants in 2020-2021 (follow-up) with a different collection method. The aims of this thesis were to compare the bacterial composition of gingiva and saliva samples collected at baseline and study longitudinal changes in bacterial composition of saliva samples collected at baseline and follow-up. Test saliva samples were collected to determine if the different collection methods could interfere with the sequencing results, and thereby affect the comparison of baseline and follow-up saliva. A pilot study was designed and performed on eight of the test saliva samples to detect the presence and investigate the composition of archaea. Bacterial community profiling was performed by amplicon sequencing of the V1-V2 (gingiva) or V3-V4 (saliva) regions of the 16S rRNA gene with an Illumina MiSeq sequencer. Gingiva sequencing had been performed some years ago while saliva samples were sequenced in-house as part of this master project. Bioinformatics and biostatistics were performed using QIIME2 and R. Comparisons of the gingival and salivary community profiles showed that the taxonomic composition of bacteria in gingiva is distinct from saliva. Baseline and follow-up samples were also found to be distinct from each other in terms of taxonomy, alpha diversity and beta diversity. Differences in the bacterial composition of baseline and follow-up samples could not be attributed to collection method, since the test samples collected to assess this were similar in terms of taxonomy, alpha diversity and beta diversity. The archaeal composition of saliva has not been analysed yet, but the PCR and sequencing reads confirm that one of the tested sets of archaea-specific primer pairs was successful in recovering archaea from saliva samples.