Microbial Community Profiling Using Terminal Restriction Fragment Length Polymorphism (T-RFLP) and Denaturing Gradient Gel Electrophoresis (DGGE)
In their natural environments, microorganisms usually live in organized communities. Profiling analysis of microbial communities has recently assumed special relevance as it allows a thorough understanding of the diversity of the microbiota, its behavior over time, and the establishment of patterns associated with health and disease. The application of molecular biology approaches holds the advantage of including culture-difficult and as-yet-uncultivated phylotypes in the profiles, providing a more comprehensive picture of the microbial community. This chapter focuses on two particular techniques, namely, terminal restriction fragment length polymorphism (T-RFLP) and denaturing gradient gel electrophoresis (DGGE), both of which have been widely used in environmental studies and have been successfully used by the authors in the study of the oral microbial communities associated with conditions of health and disease.
Key wordsHuman oral microbiota 16S rRNA gene Terminal restriction fragment length polymorphism (T-RFLP) Denaturing gradient gel electrophoresis (DGGE)
This work was supported in part by grants from the Brazilian National Research Council (CNPq) and FAPERJ (José Siqueira and Alexandre Rosado) and by a Grant-in-Aid for Scientific Research (No. 13672202) from the Japan Society for the Promotion of Science (Mitsuo Sakamoto). We are grateful to Natalia Franco for drawing the DGGE schemes.
- 10.Machado de Oliveira JC, Siqueira JF Jr, Rôças IN, Baumgartner JC, Xia T, Peixoto RS, Rosado AS (2007) Bacterial community profiles of endodontic abscesses from Brazilian and USA subjects as compared by denaturing gradient gel electrophoresis analysis. Oral Microbiol Immunol 22:14–18CrossRefPubMedGoogle Scholar