Willem de Vos

11 – Molecular Characterisation of Microbial Communities Based on 16S rRNA Sequence Diversity

The application of Temperature Gradient Gel Electrophoresis (TGGE), Denaturing Gradient Gel Electrophoresis (DGGE), and Single Strand Conformation Polymorphism (SSCP) to studies in microbial ecology is growing and the future perspectives are promising. The combination of reverse transcriptase-PCR, cloning, and fingerprinting of environmental samples may give an accurate description of a community. The power of these techniques is their reliability, speed, and ease of use. TGGE, DGGE, and SSCP are ideal for studying the temporal and spatial variation in microbial communities, both qualitatively and quantitatively. The only time-consuming aspect is the identification of specific amplicons in the profiles. The approach of combining 16S rDNA profiles and profiles of functional genes may enable the structure to be related to the function of an ecosystem. Another variant of this approach is the use of oligonucleotide microchips. The fingerprinting approach has already demonstrated that the dominant microbial community in adults is quite stable with time and differs for each individual. This approach can also be used to monitor the fate of certain bacteria, such as probiotic strains in the intestine. The impact of these strains on the microbial community in the gastrointestinal tract can be analyzed by quantifying similarities between the profiles or calculating microbial diversity and richness indices from profiles. Changes in band positions can be identified using cloning and sequencing analysis. The introduction of internal standards to the profiles may help the changes to be monitored quantitatively. These approaches will help in gaining an understanding of some aspects of the microbial community in the intestine.