Culturomics: Deciphering the Microbial Dark Matter in the Oral Cavity

Abstract

The idea of the tree of life originated in the 19th century and has steadily evolved since then. In the last 20 y, high-throughput sequencing methods have revolutionized microbial ecology and expanded our understanding of this tree of life tremendously. However, this has led to a sharp increase in what is known as microbial dark matter, consisting of bacterial and archaeal taxa that are only known by sequencing and have not yet been cultivated. The lack of ecologic information about these species poses a major challenge. This has led to the need for other approaches to supplement the DNA sequence–based findings. The term “culturomics”—which describes the large-scale isolation, culture, and identification of species from an environment—was introduced in 2012 with a focus on the human gut microbiota. The cultivation of new species, which had been neglected for many years, is now firmly back in the spotlight since strains are required for experimental studies to complement the knowledge obtained from microbial DNA sequences. Laboratory culture is essential to gain knowledge of microbial physiology, assign functions to novel genes and proteins, identify resistance profiles, and better understand the impact of different microorganisms on human health. While many culturomics studies have focused on gut microbiota, significant progress has been made in oral microbiology, with the enrichment of Candidatus Nanosynbacter lyticus representing one of the greatest achievements. This review gives a comprehensive overview of the oral microbial community regarding the microbial dark matter and summarizes the work carried out to date on the oral microbiota using culturomics. The capability and challenges of metagenomics and culturomics and the potential use of artificial intelligence are examined, with insights from extensive culturomics research on gut microbiota, which promises applicability to the field of oral microbiology.