The species diversity of microbial consortia differs dramatically depending on their environmental conditions. The diversity of microbial species is usually deduced based on 16S RDNA sequences amplified by polymerase chain reaction (PCR) with a universal primer set and met genomic DNA isolated using a culture-independent method from diverse environments. However, because 16S rDNA sequences themselves contain no information related to the species, phylogenetic groupings based on these data do not refer to species but to operational taxonomic units (OTUs). Considering that culturable microbes constitute less than 1%–10% of all microbes thriving in natural environments, metagenomic analysis is one of the most powerful ways to understand species and functional diversity in whole microbial communities