title: Discrimination of the Lactobacillus acidophilus group using sequencing, species-specific PCR and SNaPshot mini-sequencing technology based on the recA gene.
abstract: BACKGROUND
  To clearly identify specific species and subspecies of the Lactobacillus acidophilus group using phenotypic and genotypic (16S rDNA sequence analysis) techniques alone is difficult. The aim of this study was to use the recA gene for species discrimination in the L. acidophilus group, as well as to develop a species-specific primer and single nucleotide polymorphism primer based on the recA gene sequence for species and subspecies identification.
  
  
  RESULTS
  The average sequence similarity for the recA gene among type strains was 80.0%, and most members of the L. acidophilus group could be clearly distinguished. The species-specific primer was designed according to the recA gene sequencing, which was employed for polymerase chain reaction with the template DNA of Lactobacillus strains. A single 231-bp species-specific band was found only in L. delbrueckii. A SNaPshot mini-sequencing assay using recA as a target gene was also developed. The specificity of the mini-sequencing assay was evaluated using 31 strains of L. delbrueckii species and was able to unambiguously discriminate strains belonging to the subspecies L. delbrueckii subsp. bulgaricus.
  
  
  CONCLUSIONS
  The phylogenetic relationships of most strains in the L. acidophilus group can be resolved using recA gene sequencing, and a novel method to identify the species and subspecies of the L. delbrueckii and L. delbrueckii subsp. bulgaricus was developed by species-specific polymerase chain reaction combined with SNaPshot mini-sequencing.
authors.affiliation: Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 30062, Taiwan, ROC. chh@firdi.org.tw
authors.forename: Chien-Hsun
authors.initials: CH
authors.lastname: Huang
authors.forename: Mu-Tzu
authors.initials: MT
authors.lastname: Chang
authors.forename: Mu-Chiou
authors.initials: MC
authors.lastname: Huang
authors.forename: Li-Tin
authors.initials: LT
authors.lastname: Wang
authors.forename: Lina
authors.initials: L
authors.lastname: Huang
authors.forename: Fwu-Ling
authors.initials: FL
authors.lastname: Lee
mesh_terms: D015373:Bacterial Typing Techniques / Q000379:methods; D001483:Base Sequence; D017931:DNA Primers; D004269:DNA, Bacterial / Q000032:analysis; D004275:DNA, Ribosomal / Q000032:analysis; D005798:Genes, Bacterial; D005838:Genotype; D007779:Lactobacillus acidophilus / Q000235:genetics*; D008969:Molecular Sequence Data; D010641:Phenotype; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D011938:Rec A Recombinases / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D017385:Sequence Homology; D013045:Species Specificity
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D011938:Rec A Recombinases