Culturomics: Deciphering the Microbial Dark Matter in the Oral Cavity

Area of Science:

• Microbial Ecology
• Genomics
• Biotechnology

Background:

• High-throughput sequencing has expanded the Tree of Life but increased "microbial dark matter"—uncultured species lacking ecological data.
• Cultivation of microbial species was historically neglected but is now vital for experimental validation and functional understanding.
• Oral microbiology faces challenges in characterizing the vast uncultured microbial community.

Purpose of the Study:

• To provide a comprehensive overview of oral microbial communities, focusing on microbial dark matter.
• To summarize current culturomics research in oral microbiology.
• To examine the capabilities and challenges of metagenomics and culturomics in oral microbiology, considering AI applications.

Main Methods:

• Culturomics: large-scale isolation, culture, and identification of microbial species.
• Metagenomic analysis to complement cultivation-based findings.
• Review of existing literature on oral microbiota and culturomics.

Main Results:

• Culturomics has successfully enriched previously uncultured species, such as *Candidatus* Nanosynbacter lyticus in oral studies.
• Significant progress has been made in applying culturomics to oral microbiology, complementing DNA sequencing data.
• Challenges remain in culturing diverse oral microbes, but advancements are promising.

Conclusions:

• Culturomics is essential for understanding microbial physiology, gene function, and health impacts, especially for uncultured species.
• The application of culturomics to oral microbiology is expanding, offering new insights into the oral microbiome.
• Integrating culturomics with metagenomics and artificial intelligence holds great potential for advancing oral microbiology.