If identification to the species-level taxonomic hierarchy is enough, then a 16S rRNA gene sequence analysis would suffice. For pure culture, a PCR with university primers (such as 27F, pA, 799f with 1525R, 907R, 1429R respectively) and sequencing followed by BLASTn would do. For mixed culture, you can once again look into 16S rRNA either after cloning, or if you have a very complex mix DGGE or tag pyrosequencing. However, please note that 16S based DGGE nor pyrosequencing would give you a reliable species level identities.
If identification to the species-level taxonomic hierarchy is enough, then a 16S rRNA gene sequence analysis would suffice. For pure culture, a PCR with university primers (such as 27F, pA, 799f with 1525R, 907R, 1429R respectively) and sequencing followed by BLASTn would do. For mixed culture, you can once again look into 16S rRNA either after cloning, or if you have a very complex mix DGGE or tag pyrosequencing. However, please note that 16S based DGGE nor pyrosequencing would give you a reliable species level identities.
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