With the advent of meta-genomics methods, the entire community of microorganisms that exist in a given environment can potentially be identified. Pyrosequencing and other high throughput sequencing approaches have been applied to determine the microbial population in environmental samples such as soil and seawater [8] [9] [10] [11] and more recently to investigate the community of microbes on human mucosal surfaces [12] [13] [14] [15] , both of which are rich in microorganisms. Next generation sequencing methods have also been successfully applied to identify the microbial agents of several new diseases [16] [17] [18] [19] [20] . Recently, RNA based meta-transcriptomic studies [21] [22] [23] , which profile both protein-coding transcripts and ribosomal RNA (rRNA), have been used to study both functional and structural features of environmental microbial communities.