Metagenomics provides information on the total genetic structure and functional composition of nondisposing samples of microbial environments without the need to culture the microorganisms in the community. Metagenomics currently capitalizes on the wide variety of whole gene sequences currently known (1, 2 ) and related methods, such as bacterial artificial chromosomes and fosmid vectors, to discover new genes and study the structure and function of microbial communities. In comparative genomic studies, a number of complementary and more inexpensive methods can be used to compare the genomes of different microorganisms. Suppressive subtractive hybridization (S S H ) is one such method that can be used to compare the genome composition of closely related species of microorganisms (3-6). Recently, S S H has also been used as a comparative method to study microbial diversity and functional differences in the genetic composition of two different rumen microbial communities (7). After a series of hybridizations and polymerase chain reaction (P C R ) amplifications, metagenomic differences between the two environmental samples could be separated by the S S H method. These differences were finally characterized by sequence D N A determination and bioinformatics analysis.

Written by Martin, this experiment is from "Environmental Genomics Lab Guide".

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