Multi-Loci Gene Sequencing and Identification of Bifidobacteria Strains Isolated from Dairy and Pharmaceutical Sources in South Africa

The 16S rRNA gene sequence analysis of Bifidobacterium species reveals high interspecies sequence similarity in the range of 87.7–99.5%. This study illustrated the extent of superiority of a multigenic approach, involving protein-coding genes, in comparison to the 16S rRNA gene, to precisely delineate presumptive Bifidobacterium isolates obtained from probiotic milk beverages, culture collections and pharmaceutical probiotic preparations. Oligonucleotide pairs PurF-rev/PurF-uni; RpoC-uni/RpoC-rev; DnaB-uni/DnaB-rev; DnaG-uni/DnaG-rev; and ClpC-uni/ClpC-rev amplified housekeeping genes while 27F/1492R amplified the 16S rRNA gene of the presumptive bifidobacteria in a polymerase chain reaction. Sequences of 16S rRNA gene and some protein-coding genes effectively identified the isolates. Phylogenetic analysis together with concatenation showed that clpC, purF and dnaG genes had over 8-fold better discriminatory power than the 16S rRNA gene in discriminating between Bifidobacterium isolates. However, phylogenetic analysis involving dnaB and rpoC gene sequences or their concatenated trees showed discrepancies in clustering isolates with designated type strains.