Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023:2588:105-130.
doi: 10.1007/978-1-0716-2780-8_8.

Bioinformatic Approaches for Describing the Oral Microbiota

Kristi Biswas  1 , Michael W Taylor  2 , David T J Broderick  3   2
Affiliations

Bioinformatic Approaches for Describing the Oral Microbiota

Kristi Biswas et al. Methods Mol Biol. 2023.

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.

PubMed Disclaimer

References

    1. Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R (2018) Current understanding of the human microbiome. Nat Med 24(4):392–400 - DOI
    1. Sedghi L, DiMassa V, Harrington A, Lynch SV, Kapila YL (2021) The oral microbiome: role of key organisms and complex networks in oral health and disease. Periodontol 2000 87(1):107–131 - DOI
    1. Abellan-Schneyder I, Matchado MS, Reitmeier S, Sommer A, Sewald Z, Baumbach J et al (2021) Primer, pipelines, parameters: issues in 16S rRNA gene sequencing. mSphere 6(1):e01202–e01220 - DOI
    1. Vesty A, Biswas K, Taylor MW, Gear K, Douglas RG (2017) Evaluating the impact of DNA extraction method on the representation of human oral bacterial and fungal communities. PLoS One 12(1):e0169877 - DOI
    1. Quince C, Walker AW, Simpson JT, Loman NJ, Segata N (2017) Shotgun metagenomics, from sampling to analysis. Nat Biotechnol 35(9):833–844 - DOI

MeSH terms

Substances

LinkOut - more resources