Microbial phylogeny and diversity: Small subunit ribosomal RNA sequence analysis and beyond

Small subunit ribosomal RNA (16S rRNA) gene sequence analysis is used for the identification and classification of prokaryotes. In addition, sequencing of 16S rRNA genes amplified directly from the environment is used to estimate microbial diversity. The presence of mosaicism, intra-genomic heterogeneity and the lack of a universal threshold sequence identity value limit 16S rRNA-based phylogenetic analysis. PCR-amplification bias and cloning bias can also result in an inaccurate representation of the microbial diversity. In this review, recently reported complexities of 16S rRNA gene sequence analyses and the requirement of additional tools for microbial phylogeny and diversity analyses are discussed.