doi: 10.1099/ijs.0.019307-0, Charteris, W. P., Kelly, P. M., Morelli, L., and Collins, J. K. (2001). This has a possibility that ‘L. (2016). Int. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. 48, 2629–2638. The diversity of lactic acid bacteria in a traditional Taiwanese millet alcoholic beverage during fermentation. Rev. J. MALDI-TOF MS is straightforward, rapid, accurate, and inexpensive (although the initial outlay for the instrument is considerable), and it has high throughput (Neville et al., 2011; Sandrin et al., 2013; Tran et al., 2015). Evol. As of May 2018, it consists of 196 validly published species1, and these species are commonly isolated not only from environments associated with fermented food, such as fruits, meat, sourdough, vegetables, and wine, but also from the gastrointestinal and vaginal tracts of humans and animals (Watanabe et al., 2008; Hammes and Hertel, 2009; Pot et al., 2014; Tamang et al., 2015). The reference strains of L. casei group were used to validate the in-house database. The specificity of this assay was evaluated using 63 L. casei group strains. 62, 489–494. (2006). Huang et al. doi: 10.1002/jsfa.3658, Huang, C.-H., and Lee, F.-L. (2011). (2014). doi: 10.1128/mSystems.00061-17, Yanokura, E., Oki, K., Makino, H., Modesto, M., Pot, B., Mattarelli, P., et al. B. BMC Bioinformatics 14:60. doi: 10.1186/1471-2105-14-60, Meier-Kolthoff, J. P., Klenk, H.-P., and Göker, M. (2014). nov., and Weissella bombi sp. Mattarelli et al. MALDI-TOF MS can typically discriminate between bacterial strains at both the genus and species levels using proteomics-based identification, and subspecies- and strain-level taxonomic resolution is possible when the method is combined with specific mass spectral (MS) peaks (Spinali et al., 2015). Lactobacillus casei is one of the many species of bacteria belonging in the genus Lactobacillus. Microbiol. This is subsequently the foundation used to define the housekeeping genes (dnaJ, dnaK, mutL, pheS, and yycH) used to ascertain the species level of the strain by MLSA. Antonie Van Leeuwenhoek 97, 289–296. 43, 5309–5311. DDH has long been used as a method for delineation of bacterial species because of its status as a conventional gold standard genotypic assay (Wayne et al., 1987; Stackebrandt et al., 2002). 89, 3345–3351. Microbiol. Food Sci. J. Syst. Lett. (2013). 66, 1100–1103.  |  mSystems 2, e00061-e17. nov. Syst. J. Oncol. Biol. A split network tree based on the fragmented all-against-all comparison of the whole genome sequences using Gegenees software to separate the novel strains and four type strains in the L. casei group could be separated into four clusters: Cluster A consisting of L. casei ATCC 393T (Accession No. Please enable it to take advantage of the complete set of features! Despite this being a hot topic, as demonstrated by the large amount of literature about it, the results of different proposed identification methods are often ambiguous and unsatisfactory. Rapid species-level identification of vaginal and oral lactobacilli using MALDI-TOF MS analysis and 16S rDNA sequencing. zeae’ was designed by Desai et al. nov., isolated from human faeces. Evol. doi: 10.1016/j.fm.2016.05.004, Sato, H., Teramoto, K., Ishii, Y., Watanabe, K., and Benno, Y. doi: 10.1007/s00217-012-1712-0, Zeigler, D. R. (2003). However, the results of polyphasic characterization implied that the current L. casei group has at least four distinct species; L. casei, L. chiayiensis sp. Numerals in parentheses under strain name are the numbers of the predicted ORFs. Lactobacillus casei,Lactobacillus paracasei and Lactobacillusrhamnosus form a closely related taxonomic group (the L. casei group) within the facultatively heterofermentative lactobacilli. Ortholog analysis among six type strains in the L. casei group. Front. (2006). (2018). Evol. However, horizontal gene transfer (HGT) or lateral gene transfer may cause problems in phylogenetic tree construction based on a single gene. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. However, reference databases are mainly designed for routine clinical practice (Bizzini and Greub, 2010), and expansion of the database is necessary to increase identification rates through matching. Syst. Probiotics as efficient immunopotentiators: translational role in cancer prevention. 29, 90–92. Food Res. Microbiol. Cell. A combination of RAPD-PCR and the SCAR technique has been applied to develop the species- and subspecies-specific primers for L. paracasei subsp. nov., four novel heterofermentative species isolated from sunki, a Japanese traditional pickle. Strains of these species have been used for a long time as probiotics in a wide range of products, and they represent the dominant species of nonstarter lactic acid bacteria in ripened cheeses, where they contribute to flavour development. 76, M568–M572. doi: 10.4056/sigs.531120, Bizzini, A., and Greub, G. (2010). Importance of lactobacilli in food and feed biotechnology. zeae’ within the L. casei group (Huang and Lee, 2009). DNA sequence-based analysis of the Pseudomonas species. Int. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. eCollection 2018. nov., isolated from the faeces of piglets. 19, 2226–2238. Appl. casei, and forbade the name L. paracasei. J. Syst. Therefore, a method that quickly and accurately identifies starter cultures is required for the management and quality control of commercial probiotic products. doi: 10.1099/00207713-41-2-340, Desai, A. R., Shah, N. P., and Powell, I. Res. Analyst 141, 2827–2837. Leuconostoc holzapfelii sp. 161, 480–487. nov., from a Ghanaian cocoa fermentation. Int. Food Microbiol. (1980). This similarity in phenotypic traits may be influenced by the possible acquisition or depletion of plasmids encoding large number of carbohydrate fermentation traits or environmental conditions, and this may result in isolates with metabolic features that are atypical (Ahrné et al., 1989), rendering the established identification methods laborious and imprecise. Stand. doi: 10.1002/1521-4028(200110)41:5<241::AID-JOBM241>3.0.CO;2-2, Chen, Y.-S., Wang, L.-T., Liao, Y.-J., Lan, Y.-S., Chang, C.-H., Chang, Y.-C., et al. Microbiol. (Berlin: Springer), 465–510. zeae’ has a possibility to be reclassified as the independent new taxon. 81, 1520–1529. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. During a study whose objective was to isolate lactobacilli from different environmental samples, strain BCRC 81062T was isolated from cow manure collected in Chiayi, Taiwan. Microbiol. Arch Latinoam Nutr. MALDI-TOF identification of the human gut microbiome in people with and without diarrhea in Senegal. Identification and typing of Lactococcus lactis by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Minor differences in the proteome of Bacillus subtilis and Bacillus mojavensis based upon high abundance/conserved protein mass spectra; implications for rapid, improved identification of two pathogen genetically closely related. doi: 10.1007/s12602-012-9117-8, Samb-Ba, B., Mazenot, C., Gassama-Sow, A., Dubourg, G., Richet, H., Hugon, P., et al. casei and rejection of the name Lactobacillus paracasei (Collins et al., 1989). SCARs are detected by PCR using specific primers designed based on the sequence data of RAPD fragment. Whole-genome-based comparisons, such as ANI and dDDH, have become the gold standards for demarcation of phylogenetic relationships as well as for delineating new species; these methods can replace traditional DDH, conventional determination of DNA G+C content, and 16S rRNA and housekeeping genes sequencing.

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