Bioinformatic Approaches for Describing the Oral Microbiota

Kristi Biswas; Michael W Taylor; David T J Broderick

doi:10.1007/978-1-0716-2780-8_8

Bioinformatic Approaches for Describing the Oral Microbiota

Methods Mol Biol. 2023:2588:105-130. doi: 10.1007/978-1-0716-2780-8_8.

Authors

Kristi Biswas¹, Michael W Taylor², David T J Broderick^{3

2}

Affiliations

¹ Department of Surgery, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand. k.biswas@auckland.ac.nz.
² School of Biological Sciences, University of Auckland, Auckland, New Zealand.
³ Department of Surgery, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.

PMID: 36418685
DOI: 10.1007/978-1-0716-2780-8_8

Abstract

Cultivation-independent (molecular) analysis of the oral microbiota can provide a comprehensive picture of microbial community composition, yet there is an at-times bewildering array of approaches that can be employed. This chapter introduces some of the key considerations when undertaking microbiota research and describes two alternative bioinformatic pipelines for conducting such studies. The descriptions are based on analysis of bacterial 16S ribosomal RNA gene sequences, but can be easily adapted for analysis of other microbial taxa such as fungi.

Keywords: 16S rRNA gene sequencing; Bacterial community; Bioinformatic analysis; DADA2; Microbial diversity; Oral microbiota; QIIME2.

MeSH terms

Computational Biology*
Microbiota* / genetics
RNA, Ribosomal, 16S / genetics

Substances

RNA, Ribosomal, 16S