Comprehensive evaluation of microbial diversity in almost any environment is now possible. Questions such as "Does the addition of fiber to the diet of humans change the gastrointestinal microbiota?" can now be answered easily and inexpensively. Tag-encoded FLX-amplicon pyrosequencing (TEFAP) has been utilized to evaluate bacterial, archaeal, fungal, algal, as well as functional genes. Using the new tag-encoded FLX amplicon pyrosequencing (bTEFAP) approach, we have evaluated the microbial diversity using a more cost-effective and largely reproducible method that would allow us to sequence the ribosomal RNA genes of microorganisms (hereafter focused on bacteria), without the need for the inherent bias of culture methods. These developments have ushered in a new age of microbial ecology studies, and we have utilized this technology to evaluate the microbiome in a wide range of systems in almost any conceivable environment.