As a result of advancements in high-throughput technology, the sequencing of the pioneering 16S rRNA gene marker is gradually shedding light on the taxonomic characterization of the spectacular microbial diversity that inhabits the earth. 16S rRNA-based investigations of microbial environmental niches are currently conducted using several technologies, including large-scale clonal Sanger sequencing, oligonucleotide microarrays, and, particularly, 454 pyrosequencing that targets specific regions or is linked to barcoding strategies. Interestingly, the short read length produced by next-generation sequencing technology has led to new computational efforts in the taxonomic sequence assignment process. From a medical perspective, the characterization of the microbial composition of the skin surface, oral cavity, and gut in both healthy and diseased people enables a comparison of microbial community profiles and also contributes to the understanding of the potential impact of a particular microbial community.