The dnaJ gene as a molecular discriminator to differentiate among species and strain within the Lactobacillus casei group

Salvetti, 2012, The genus Lactobacillus: a taxonomic update, Probiotics Antimicrob. Proteins, 4, 217, 10.1007/s12602-012-9117-8 Tindall, 2008, Int. J. Syst. Evol. Microbiol., 58, 1764, 10.1099/ijs.0.2008/005330-0 Holzapfel, 2001, Taxonomy and important features of probiotic microorganisms in food and nutrition, Am. J. Clin. Nutr., 73, 365S, 10.1093/ajcn/73.2.365s Huys, 2006, Accuracy of species identity of commercial bacterial cultures intended for probiotic or nutritional use, Res. Microbiol., 157, 803, 10.1016/j.resmic.2006.06.006 FAO/WHO, 2002 Boyd, 2005, Comparison of API 50 CH strips to whole-chromosomal DNA probes for identification of Lactobacillus species, J. Clin. Microbiol., 43, 5309, 10.1128/JCM.43.10.5309-5311.2005 Bringel, 2005, Lactobacillus plantarum subsp. argentoratensis subsp. nov., isolated from vegetable matrices, Int. J. Syst. Evol. Microbiol., 55, 1629, 10.1099/ijs.0.63333-0 Charteris, 2001, Quality control of Lactobacillus strains for use with the API 50CH and API ZYM systems at 37 degrees C, J. Basic Microbiol., 41, 541, 10.1002/1521-4028(200110)41:5<241::AID-JOBM241>3.0.CO;2-2 Ahrne, 1989, Plasmids in Lactobacillus strains isolated from meat and meat products, Syst. Appl. Microbiol., 11, 320, 10.1016/S0723-2020(89)80031-1 Pot, 1993, Identification and classification of Lactobacillus acidophilus, L. gasseri and L. johnsonii strains by SDS-PAGE and rRNA-targeted oligonucleotide probe hybridization, J. Gen. Microbiol., 139, 513, 10.1099/00221287-139-3-513 Walter, 2000, Detection and identification of gastrointestinal Lactobacillus species by using denaturing gradient gel electrophoresis and species-specific PCR primers, Appl. Environ. Microbiol., 66, 297, 10.1128/AEM.66.1.297-303.2000 Roy, 1999, Strain identification of probiotic Lactobacillus casei related isolates with randomly amplified polymorphic DNA and pulsed-field gel electrophoresis methods, Biotechnol. Tech., 13, 843, 10.1023/A:1008952023716 Huang, 2009, Development of novel species-specific primers for species identification of the Lactobacillus casei group based on the RAPD fingerprints, J. Sci. Food Agric., 89, 1831, 10.1002/jsfa.3658 Gancheva, 1999, A polyphasic approach towards the identification of strains belonging to Lactobacillus acidophilus and related species, Syst. Appl. Microbiol., 22, 573, 10.1016/S0723-2020(99)80011-3 Gevers, 2001, Applicability of rep-PCR fingerprinting for identification of Lactobacillus species, FEMS Microbiol. Lett., 205, 31, 10.1111/j.1574-6968.2001.tb10921.x Massi, 2004, Identification method based on PCR combined with automated ribotyping for tracking probiotic Lactobacillus strains colonizing the human gut and vagina, J. Appl. Microbiol., 96, 777, 10.1111/j.1365-2672.2004.02228.x Collins, 1989, Deoxyribonucleic acid homology studies of Lactobacillus casei, Lactobacillus paracasei sp. nov., subsp. paracasei and subsp. tolerans, and Lactobacillus rhamnosus sp. nov., comb. nov, Int. J. Syst. Bacteriol., 39, 105, 10.1099/00207713-39-2-105 Petti, 2005, The role of 16S rRNA gene sequencing in identification of microorganisms misidentified by conventional methods, J. Clin. Microbiol., 43, 6123, 10.1128/JCM.43.12.6123-6125.2005 Stackebrandt, 2006, Taxonomic parameters revisited: tarnished gold standards, Microbiol. Today, 33, 152 Stackebrandt, 2002, Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology, Int. J. Syst. Evol. Microbiol., 52, 1043 Qiu, 2006, The diversity of the DnaJ/Hsp40 family, the crucial partners for Hsp70 chaperones, Cell. Mol. Life Sci., 63, 2560, 10.1007/s00018-006-6192-6 Alexandre, 2008, dnaJ is a useful phylogenetic marker for alphaproteobacteria, Int. J. Syst. Evol. Microbiol., 58, 2839, 10.1099/ijs.0.2008/001636-0 Thompson, 1997, The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucleic Acids Res., 25, 4876, 10.1093/nar/25.24.4876 Campanella, 2003, MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences, BMC Bioinform., 4, 29, 10.1186/1471-2105-4-29 Felsenstein, 1993 Saitou, 1987, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol., 4, 406 Kimura, 1980, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, J. Mol. Evol., 16, 111, 10.1007/BF01731581 Librado, 2009, DnaSP v5: A software for comprehensive analysis of DNA polymorphism data, Bioinformatics, 25, 1451, 10.1093/bioinformatics/btp187 Huang, 2014, Molecular discrimination and identification of Acetobacter genus based on the partial heat shock protein 60 (hsp60) sequences, J. Sci. Food Agric., 94, 213, 10.1002/jsfa.6231 Toh, 2013, Genomic adaptation of the Lactobacillus casei group, PLoS One, 8, e75073, 10.1371/journal.pone.0075073 Morita, 2004, Genetic diversity of the dnaJ gene in the Mycobacterium avium complex, J. Med. Microbiol., 53, 813, 10.1099/jmm.0.45601-0 Itoh, 2006, dnaJ and gyrB gene sequence relationship among species and strains of genus Streptococcus, Syst. Appl. Microbiol., 29, 368, 10.1016/j.syapm.2005.12.003 Shah, 2007, dnaJ gene sequence-based assay for species identification and phylogenetic grouping in the genus Staphylococcus, Int. J. Syst. Evol. Microbiol., 57, 25, 10.1099/ijs.0.64205-0 Nhung, 2007, The dnaJ gene as a novel phylogenetic marker for identification of Vibrio species, Syst. Appl. Microbiol., 30, 309, 10.1016/j.syapm.2006.11.004 Zhang, 2011, DnaJ sequences of Bacillus cereus strains isolated from outbreaks of hospital infection are highly similar to Bacillus anthracis, Diagn. Microbiol. Infect. Dis., 70, 307, 10.1016/j.diagmicrobio.2011.02.012 Felis, 2001, Comparative sequence analysis of a recA gene fragment brings new evidence for a change in the taxonomy of the Lactobacillus casei group, Int. J. Syst. Evol. Microbiol., 51, 2113, 10.1099/00207713-51-6-2113 Huang, 2014, Use of highly variable gene (yycH) as DNA marker to resolve interspecific relationships within the Lactobacillus casei group and a target for developing novel species-specific PCR primers, Eur. Food Res. Technol., 239, 719, 10.1007/s00217-014-2278-9 Huang, 2011, The dnaK gene as a molecular marker for the classification and discrimination of the Lactobacillus casei group, Antonie Leeuwenhoek, 99, 319, 10.1007/s10482-010-9493-6 Naser, 2007, Identification of lactobacilli by pheS and rpoA gene sequence analyses, Int. J. Syst. Evol. Microbiol., 57, 2777, 10.1099/ijs.0.64711-0 Cai, 2007, Genotypic and phenotypic characterization of Lactobacillus casei strains isolated from different ecological niches suggests frequent recombination and niche specificity, Microbiology, 153, 2655, 10.1099/mic.0.2007/006452-0 Parolo, 2011, Genetic diversity of Lactobacillus paracasei isolated from in situ human oral biofilms, J. Appl. Microbiol., 111, 105, 10.1111/j.1365-2672.2011.05041.x Krawczyk, 2002, Comparative studies of the Acinetobacter genus and the species identification method based on the recA sequence, Mol. Cell. Probes, 16, 1, 10.1006/mcpr.2001.0388 Huang, 2012, Discrimination of the Lactobacillus acidophilus group using sequencing, species-specific PCR and SNaPshot mini-sequencing technology based on the recA gene, J. Sci. Food Agric., 92, 2703, 10.1002/jsfa.5692 Huang, 2011, Application of the SNaPshot minisequencing assay to species identification in the Lactobacillus casei group, Mol. Cell. Probes, 25, 153, 10.1016/j.mcp.2011.03.002 Huang, 2011, Rapid identification of Lactobacillus plantarum group using the SNaPshot minisequencing assay, Syst. Appl. Microbiol., 34, 586, 10.1016/j.syapm.2011.02.006 Nikolausz, 2009, Evaluation of single-nucleotide primer extension for detection and typing of phylogenetic markers used for investigation of microbial communities, Appl. Environ. Microbiol., 75, 2850, 10.1128/AEM.01910-08