Comparative evaluation of microbial profiles of oral samples obtained at different collection time points and using diff
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ORIGINAL ARTICLE
Comparative evaluation of microbial profiles of oral samples obtained at different collection time points and using different methods Michi Omori 1 & Nahoko Kato-Kogoe 1 & Shoichi Sakaguchi 2 & Nozomu Fukui 1 & Kayoko Yamamoto 1 & Yoichiro Nakajima 1 & Kazuya Inoue 1 & Hiroyuki Nakano 1 & Daisuke Motooka 3 & Takashi Nakano 2 & Shota Nakamura 3 & Takaaki Ueno 1 Received: 10 August 2019 / Accepted: 15 September 2020 # Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Objectives Recently, the oral microbiome has been found to be associated with oral and general health status. Although various oral sample collection protocols are available, the potential differences between the results yielded by these protocols remain unclear. In this study, we aimed to determine the effects of different time points and methods of oral sample collection on the outcomes of microbiome analysis. Materials and methods Oral samples were collected from eight healthy individuals at four different time points: 2 h after eating, immediately after teeth brushing, immediately after waking up, and 2 h after eating on the subsequent day. Four methods of saliva collection were evaluated: spitting, gum chewing, cotton swab, and oral rinse. Oral microbiomes of these samples were compared by analyzing the bacterial 16S rRNA gene sequence data. Results The oral microbial composition at the genus level was similar among all sample collection time points and methods. Alpha diversity was not significantly different among the groups, whereas beta diversity was different between the spitting and cotton swab methods. Compared with the between-subject variations, the weighted UniFrac distances between the groups were not minor. Conclusions Although the oral microbiome profiles obtained at different collection time points and using different methods were similar, some differences were detected. Clinical relevance The results of the present study suggest that although all the described protocols are useful, comparisons among microbiomes of samples collected by different methods are not appropriate. Researchers must be aware of the issues regarding the impact of saliva collection methods. Keywords Human . Metagenome . Methods . Microbiota . Saliva
Introduction * Nahoko Kato-Kogoe [email protected] 1
Department of Dentistry and Oral Surgery, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki City, Osaka 569-8686, Japan
2
Department of Microbiology and Infection Control, Osaka Medical College, Takatsuki, Osaka, Japan
3
Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
Current advances in next-generation sequencing technology and associated bioinformatics tools have led to the efficient characterization of the full microbiome complement of biologic samples [1]. This has enabled the understanding of the association between the human microbiome and various diseases, such as autoimmune disorders, diabetes, obesity, cancer,
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