Strain-Specific Genotyping of Bifidobacterium animalis subsp. lactis by Using Single-Nucleotide Polymorphisms, Insertions, and Deletions

Abstract

Several probiotic strains of Bifidobacterium animalis subsp. lactis are widely supplemented into food products and dietary supplements due to their documented health benefits and ability to survive within the mammalian gastrointestinal tract and acidified dairy products. The strain specificity of these characteristics demands techniques with high discriminatory power to differentiate among strains. However, to date, molecular approaches, such as pulsed-field gel electrophoresis and randomly amplified polymorphic DNA-PCR, have been ineffective at achieving strain separation due to the monomorphic nature of this subspecies. Previously, sequencing and comparison of two B. animalis subsp. lactis genomes (DSMZ 10140 and Bl-04) confirmed this high level of sequence similarity, identifying only 47 single-nucleotide polymorphisms (SNPs) and four insertions and/or deletions (INDELs) between them. In this study, we hypothesized that a sequence-based typing method targeting these loci would permit greater discrimination between strains than previously attempted methods. Sequencing 50 of these loci in 24 strains of B. animalis subsp. lactis revealed that a combination of nine SNPs/INDELs could be used to differentiate strains into 14 distinct genotypic groups. In addition, the presence of a nonsynonymous SNP within the gene encoding a putative glucose uptake protein was found to correlate with the ability of certain strains to transport glucose and to grow rapidly in a medium containing glucose as the sole carbon source. The method reported here can be used in clinical, regulatory, and commercial applications requiring identification of B. animalis subsp. lactis at the strain level.

Persistence of Antibiotic Resistance: Evaluation of a Probiotic Approach Using Antibiotic-Sensitive Megasphaera elsdenii Strains To Prevent Colonization of Swine by Antibiotic-Resistant Strains

“…Diversity in both SNP identities and antibiotic susceptibility phenotypes suggests that swine intestinal M. elsdenii populations have subspecies diversity. Such diversity would be consistent with a growing number of reports of subspecies diversity among both pathogenic and nonpathogenic species colonizing the animal and human intestinal tracts (4,8,9,19,35). Our results indicate that comparable investigations could be insightful for M. elsdenii.…”

Comparative Genomics of Bifidobacterium animalis subsp. lactis Reveals a Strict Monophyletic Bifidobacterial Taxon

“…So far, several attempts have been carried out to delineate the evolutionary development of B. animalis subsp. lactis, as well as the genetic relatedness with other bifidobacterial species (14,(19)(20)(21). However, these studies drew their conclusions from a limited set of genomic information, as opposed to the much larger data set of B. animalis subsp.…”

Insights into the Ropy Phenotype of the Exopolysaccharide-Producing Strain Bifidobacterium animalis subsp. lactis A1dOxR

“…lactis genomes (23). This fact is not surprising due to the scarce genetic variability detected in the whole genomes of strains of this subspecies (24).…”