Identification using sequence analysis of housekeeping genes at BCCM/LMG

16S rDNA sequence analysis is the most commonly used method for identifying bacteria or for constructing phylogenetic trees. However, the 16S rRNA gene often shows limited taxonomic resolution to differentiate members of closely related taxa. In those cases, sequence analysis of one or more selected protein-encoding or so-called housekeeping genes can be an alternative approach. Housekeeping genes usually exhibit a higher genetic variation compared to the 16S rRNA gene, and thus enable a more accurate classification and identification of bacteria.

At BCCM/LMG, sequence analysis of housekeeping gene(s) is offered as a customer service for identification of specific groups of bacteria at (sub)species level. For unknown isolates, this implies that the genus or family identity needs to be determined before a choice of the best suited housekeeping gene(s) can be made.

The following groups and suggested genes are part of our standard portfolio:

Bacillus subtilis complex: gyrA and/or gyrB

Staphylococcus: dnaJ

Lactic acid bacteria: pheS and/or rpoA

Enterobacteriaceae: atpD, gyrB, infB and/or rpoB


This list is not limited and sequence analysis of other housekeeping gene(s)/ groups is also possible on request.

The service report includes the technical description of primer and PCR conditions and results of sequence analysis of housekeeping gene(s) performed with the BioNumerics v7.0 software program. A similarity matrix and a phylogenetic tree derived from this analysis are also included.



Brady, C., Cleenwerck, I., Venter, S., Coutinho, T., De Vos, P. (2013). Taxonomic evaluation of the genus Enterobacter based on multilocus sequence analysis (MLSA): proposal to reclassify E. nimipressuralis and E. amnigenus into Lelliottia gen. nov. as Lelliottia nimipressuralis comb. nov. and Lelliottia amnigena comb. nov., respectively, E. gergoviae and E. pyrinus into Pluralibacter gen. nov. as Pluralibacter gergoviae comb. nov. and Pluralibacter pyrinus comb. nov., respectively, E. cowanii, E. radicincitans, E. oryzae and E. arachidis into Kosakonia gen. nov. as Kosakonia cowanii comb. nov., Kosakonia radicincitans comb. nov., Kosakonia oryzae comb. nov. and Kosakonia arachidis comb. nov., respectively, and E. turicensis, E. helveticus and E. pulveris into Cronobacter as Cronobacter zurichensis nom. nov., Cronobacter helveticus comb. nov. and Cronobacter pulveris comb. nov., respectively, and emended description of the genera Enterobacter and Cronobacter. Syst Appl Microbiol 36: 309-319. doi: 10.1016/j.syapm.2013.03.005

Naser, S., Dawyndt, P., Hoste, B., Gevers, D., Vandemeulebroecke, K., Cleenwerck, I., Vancanneyt, M., Swings, J. (2007). Identification of lactobacilli by pheS and rpoA gene sequence analyses. Int J Syst Evol Microbiol 57:2777-2789. doi: 10.1099/ijs.0.64711-0

Wang, L.T., Lee, F.L., Tai, C.J., Kasai, H. (2007). Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA-DNA hybridization in the Bacillus subtilis group. Int J Syst Evol Microbiol 57:1846-50. doi: 10.1099/ijs.0.64685-0

Shah, M.M., Lihara, H., Noda, M., Song, S.X., Nhung, P.H., Ohkusu, K., Kawamura, Y., Ezaki, T. (2007). dnaJ gene sequence-based assay for species identification and phylogenetic grouping in the genus Staphylococcus. Int J Syst Evol Microbiol 57: 25-30. doi: 10.1099/ijs.0.64205-0