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 <i>Bifidobacterium</i> 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 <i>Bifidobacterium</i> 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 <i>clpC, purF</i> and <i>dnaG</i> genes had over 8-fold better discriminatory power than the 16S rRNA gene in discriminating between <i>Bifidobacterium</i> isolates. However, phylogenetic analysis involving <i>dnaB and rpoC</i> gene sequences or their concatenated trees showed discrepancies in clustering isolates with designated type strains.