| Microbial Community Analysis using RDP II (Ribosomal Database Project II):
Methods, Tools and New Advances |
| Erick Cardenas1, James R. Cole1, James M. Tiedje1,2†, and Joonhong Park2 |
1Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA
2School of Civil and Environmental Engineering, Yonsei University, Seoul, Republic of Korea |
Corresponding Author:
James M. Tiedje ,Tel: +1-517-353-9021, Fax: +1-517-353-2917, Email: tiedjej@msu.edu
|
|
Received: March 1, 2009; Accepted: March 15, 2009. |
|
|
Share : 
|
| ABSTRACT |
|
Microorganisms play an important role in the geochemical cycles, industry, environmental cleanup, and biotechnology among other fields.
Given the high microbial diversity, identification of the microorganism is essential in understanding and managing the processes. One of the most
popular and powerful method for microbial identification is comparative 16S rRNA gene analysis. Due to the highly conserved nature of this
essential gene, sequencing and later comparison of it against known rRNA databases can provide assignment of the bacteria into the taxonomy, and
the identity of its closest relatives. Isolation and sequencing of 16S rRNA genes directly from natural environments (either from DNA or RNA) can
also be used to study the structure of the whole microbial community. Nowadays, novel sequencing technologies with massive outputs are giving
researchers worldwide the chance to study the microbial world with a depth that was previously too expensive to achieve. In this article we describe
commonly used research approaches for the study of individual microorganisms and microbial communities using the tools provided by Ribosomal
Database Project website. |
| Keywords:
Microbial community analysis | Ribosomal RNA | Microbial diversity |
|
|
|
PDF Links
Full text via DOI
Download Citation 
