title: The dnaJ gene as a molecular discriminator to differentiate among species and strain within the Lactobacillus casei group.
abstract: Identifying Lactobacillus casei and its closely related taxa at the species and strain level using only phenotypic and genotypic (16S rDNA sequence homology analysis) techniques often yields inaccurate results. In this study, the dnaJ chaperone gene was investigated as a molecular target for inter- and intraspecies discrimination within the Lb. casei group as well as for the development of specific primers for species identification. The results showed that most of the examined strains could be clearly distinguished from closely related species based on the sequenced fragments. At the interspecies level, the dnaJ sequence similarities were 81.7%-85.5%. However, at the intraspecies level, the dnaJ sequence similarities were 96.2-100% and could be assigned to different haplotypes in Lactobacillus paracasei and Lactobacillus rhamnosus, respectively. Compared to the 16S rRNA gene, the dnaJ sequence showed greater variation at both the species and strain level. Thus, the dnaJ gene can be proposed as an alternative marker for the Lb. casei group that provides higher discriminatory power than the 16S rRNA gene. In addition, species-specific primers were developed and subsequently employed in two-plex minisequencing analysis and shown to be specific for Lb. paracasei and Lb. rhamnosus. Our data indicate that phylogenetic relationships in the Lb. casei group can be resolved using comparative sequence analysis of the dnaJ gene and that the Lb. paracasei and Lb. rhamnosus species can be simultaneously identified using a novel species-specific minisequencing assay.
authors.affiliation: Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Road, Hsinchu 30062, Taiwan.
authors.forename: Chien-Hsun
authors.initials: CH
authors.lastname: Huang
authors.affiliation: National Health Research Institutes, Institute of Biotechnology and Pharmaceutical Research, 35 Keyan Road, Zhunan, Miaoli County 35053, Taiwan.
authors.forename: Mu-Tzu
authors.initials: MT
authors.lastname: Chang
authors.affiliation: Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Road, Hsinchu 30062, Taiwan.
authors.forename: Lina
authors.initials: L
authors.lastname: Huang
authors.affiliation: Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Road, Hsinchu 30062, Taiwan. Electronic address: cws@firdi.org.tw.
authors.forename: Wen-Shen
authors.initials: WS
authors.lastname: Chu
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000032:analysis; D004275:DNA, Ribosomal / Q000032:analysis; D050956:HSP40 Heat-Shock Proteins / Q000235:genetics*; D007780:Lacticaseibacillus casei / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000032:analysis; D017422:Sequence Analysis, DNA / Q000379:methods; D013045:Species Specificity
chemical_list: D001426:Bacterial Proteins; D017931:DNA Primers; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D050956:HSP40 Heat-Shock Proteins; D012336:RNA, Ribosomal, 16S
keywords: Inter- and intraspecies discrimination; Lactobacillus casei group; Species-specific minisequencing; dnaJ gene