The rpoB gene encodes the β-subunit of bacterial RNA polymerase, an essential enzyme in the transcription process. This gene has been employed as a molecular marker in various microbiological contexts due to several features:

Variability: The rpoB gene offers a higher discriminatory power than the 16S rRNA gene for certain bacterial taxa, making it especially useful for differentiation at the species and strain levels.

Clinical Relevance: Mutations in the rpoB gene are associated with resistance to the antibiotic rifampicin, which is a first-line drug used to treat tuberculosis caused by Mycobacterium tuberculosis. As a result, the rpoB gene is often sequenced in clinical microbiology to detect rifampicin-resistant strains of M. tuberculosis.

Phylogenetics and Taxonomy: Due to its variability, the rpoB gene has been employed as a complementary or alternative molecular marker to the 16S rRNA gene for phylogenetic studies and bacterial identification in certain groups of bacteria.

Disease Diagnostics: In some cases, the rpoB gene has been used as a target for PCR-based detection of specific pathogens.

Overall, while the 16S rRNA gene and the ITS region remain standard tools for broad bacterial and fungal identification, respectively, the rpoB gene and other such markers offer additional or alternative options, especially when higher resolution or specific clinical insights are needed. The choice of molecular marker often depends on the specific objectives of the study or the microbial group of interest. Ripseq offers curated rpoB reference databases in case you need additional regions for better differentiation.