Using DGGE profiling to develop a novel culture medium suitable for oral microbial communities

More than 700 bacterial species have been detected in human oral cavity. They form highly organized microbial communities and are responsible for many oral infectious diseases, such as dental caries and periodontal disease. The prevention and treatment of these diseases require a comprehensive knowledge of oral microbial communities, which largely relies on culture-dependent methods to have detailed phenotypic and physiological analysis of these communities. However, most of the currently available lab media can only selectively support the growth of a limited number of bacterial species within these communities, and fail to sustain the original oral microbial diversity. In this study, using denaturing gradient gel electrophoresis (DGGE) as an index to systematically survey and analyze the selectivity of commonly used lab media, we developed a new medium (SHI medium) by combining the ingredients of several selected media which can support different sub-populations within the original oral microbial community derived from pooled saliva. DGGE and 454 pyrosequencing analysis showed that SHI medium was capable of supporting a more diversified community with a microbial profile closest to that of the original oral microbiota. Furthermore, 454 pyrosequencing revealed that SHI medium supported the growth of many oral species that have not been cultured so far. Crystal violet assay and the CLSM (confocal laser scanning microscope) analysis indicated that, compared with other media, SHI medium is able to support more complex saliva-derived biofilm with higher biomass yield and more diversified species. This DGGE-guided method could also be used to develop novel media for other complex microbial communities.