Culturing the Human Oral Microbiota, Updating Methodologies and Cultivation Techniques

Abstract

Recent years have been marked by a paradigm shift in the study of the human microbiota, with a re-emergence of culture-dependent approaches. Numerous studies have been devoted to the human microbiota, while studies on the oral microbiota still remain limited. Indeed, various techniques described in the literature may enable an exhaustive study of the microbial composition of a complex ecosystem. In this article, we report different methodologies and culture media described in the literature that can be applied to study the oral microbiota by culture. We report on specific methodologies for targeted culture and specific culture techniques and selection methodologies for cultivating members of the three kingdoms of life commonly found in the human oral cavity, namely, eukaryota, bacteria and archaea. This bibliographic review aims to bring together the various techniques described in the literature, enabling a comprehensive study of the oral microbiota in order to demonstrate its involvement in oral health and diseases.

Keywords: archaea; bacteria; culture; culturomics; fungi; human oral microbiota.

Figure 1

Phylogenetic diversity of the 19 phyla isolated or detected at least once in the human oral cavity. The number of species per phylum is presented between parents in the phylogenetic tree. The illustration on the left of the figure was made using the online tool wordle (www.wordle.net; accessed on 23 January 2023); the size of the name of each phylum is proportional to the number of species it contains. The phylogenetic tree was created using MEGA software. Figure 1 was built according to data collected from the Human Oral Microbiome Database; https://www.homd.org/; accessed on 23 January 2023.

Figure 2

Quantitative distribution of cultured and uncultured bacterial diversity composing the oral microbiota represented by number of species composing each phylum. Each phylum is represented by a different colour, as shown on the right. (Figure 2 was built according to data collected from the Human Oral Microbiome Database; https://www.homd.org/; accessed on 23 January 2023).