Abstract
Previous studies have shown that Lactobacillus futsaii (now Companilactobacillus futsaii) can be subdivided at the subspecies level. The main purpose of this study is to explore whether this is correct by using a polyphasic taxonomic approach. Lactobacillus futsaii subsp. chongqingii was proposed and effectively published in 2019. The names L. futsaii subsp. chongqingensis corrig. and Lactobacillus futsaii subsp. futsaii were not validated until March 2023. However, in the reclassification of the genus Lactobacillus by Zheng et al. in April 2020, L. futsaii was transferred to Companilactobacillus as Companilactobacillus futsaii. So Lactobacillus futsaii subsp. chongqingensis and Lactobacillus futsaii subsp. futsaii should be transferred to Companilactobacillus futsaii now. In the present study, the relationship between L. futsaii subsp. chongqingensis and L. futsaii subsp. futsaii was re-evaluated. The type strains of L. futsaii subsp. chongqingensis and L. futsaii subsp. futsaii shared identical pheS and rpoA sequences, high dDDH value, similar phenotypic characteristics and fatty acid compositions, indicating that they belonged to the same subspecies. Here, we propose to reclassify Lactobacillus futsaii subsp. chongqingensis and Lactobacillus futsaii subsp. futsaii as Companilactobacillus futsaii subsp. chongqingensis comb. nov. and Companilactobacillus futsaii subsp. futsaii comb. nov., respectively, and Companilactobacillus futsaii subsp. chongqingensis as a later heterotypic synonym of Companilactobacillus futsaii subsp. futsaii.
Abbreviations
- ANI:
-
Average nucleotide identity
- dDDH:
-
Digital DNA-DNA hybridization
- FAMEs:
-
Fatty acid methyl esters
References
Du X, Cao K, Tan M, Pan Q (2019) Lactobacillus futsaii subsp. chongqingii subsp. nov., isolated from a traditional Chinese pickle. Curr Microbiol 76:153–158. https://doi.org/10.1007/s00284-018-1601-2
Zheng J, Wittouck S, Salvetti E, Franz CMAP, Harris HMB et al (2020) A taxonomic note on the genus Lactobacillus: description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. Int J Syst Evol Microbiol 70:2782–2858. https://doi.org/10.1099/ijsem.0.004107
Oren A, Göker M (2023) Validation List no. 210. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 73:005812. https://doi.org/10.1099/ijsem.0.005812
Naser SM, Dawyndt P, Hoste B, Gevers D, Vandemeulebroecke K et al (2007) Identification of lactobacilli by pheS and rpoA gene sequence analyses. Int J Syst Evol Microbiol 57:2777–2789. https://doi.org/10.1099/ijs.0.64711-0
Xin Z, Wei X, Jiao Q, Gou Q, Zhang Y et al (2022) Whole genome sequence analysis of two subspecies of Companilactobacillus Futsaii and experimental verification of drug resistance and effect on the exploratory behavior of mice based on unique gene. PLoS ONE 17:e0274244. https://doi.org/10.1371/journal.pone.0274244
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680. https://doi.org/10.1093/nar/22.22.4673
Kishino H, Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J Mol Evol 29:170–179. https://doi.org/10.1007/BF02100115
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. https://doi.org/10.1093/molbev/msw054
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055. https://doi.org/10.1101/gr.186072.114
Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466. https://doi.org/10.1099/ijsem.0.002516
Lee I, Ouk Kim Y, Park SC, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103. https://doi.org/10.1099/ijsem.0.000760
Yoon SH, Ha S, Lim J, Kwon S, Chun J (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286. https://doi.org/10.1007/s10482-017-0844-4
Auch AF, von Jan M, Klenk H, Göker M (2010) Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117–134. https://doi.org/10.4056/sigs.531120
Davis JJ, Wattam AR, Aziz RK, Brettin T, Butler R et al (2020) The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. Nucleic Acids Res 48:D606–D612. https://doi.org/10.1093/nar/gkz943
Akopyanz N, Bukanov NO, Westblom TU, Kresovich S, Berg DE (1992) DNA diversity among clinical isolates of Helicobacter pylori detected by PCR-based RAPD fingerprinting. Nucleic Acids Res 20:5137–5142. https://doi.org/10.1093/nar/20.19.5137
Li TT, Liu DD, Fu ML, Gu CT (2020) Proposal of Lactobacillus kosoi Chiou et al. 2018 as a later heterotypic synonym of Lactobacillus micheneri McFrederick et al. 2018, elevation of Lactobacillus plantarum subsp. argentoratensis to the species level as Lactobacillus argentoratensis sp. nov., and Lactobacillus zhaodongensis sp. nov., isolated from traditional Chinese pickle and the intestinal tract of a honey bee (Apis mellifera). Int J Syst Evol Microbiol 70:3123–3133. https://doi.org/10.1099/ijsem.0.004141
Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI technical note 101. MIDI Inc, Newark
Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V et al (2014) Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 9:2. https://doi.org/10.1186/1944-3277-9-2
Jiang CS, Gu CT (2022) Companilactobacillus salsicarnum Zheng et al. 2020 is a later heterotypic synonym of Companilactobacillus mishanensis (Wei and Gu 2019) Zheng et al. 2020. Int J Syst Evol Microbiol 72:005256. https://doi.org/10.1099/ijsem.0.005256
Chao SH, Kudo Y, Tsai YC, Watanabe K (2012) Lactobacillus futsaii sp. nov., isolated from fu-tsai and suan-tsai, traditional Taiwanese fermented mustard products. Int J Syst Evol Microbiol 62:489–494. https://doi.org/10.1099/ijs.0.030619-0
Funding
This work was supported by the National Natural Science Foundation of China (No. 31471594) and “Characteristic Probiotics and New Fermented Food” Team in Northeast Agricultural University (No. 50940912, Harbin, China).
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CSJ and CTG conceived and designed the experiments. CSJ performed the experiments. CSJ and CTG analyzed the data. CSJ and CTG wrote and revised the paper.
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Jiang, CS., Gu, C.T. Proposal to Reclassify Companilactobacillus futsaii subsp. chongqingensis as a Later Heterotypic Synonym of Companilactobacillus futsaii subsp. futsaii. Curr Microbiol 81, 17 (2024). https://doi.org/10.1007/s00284-023-03541-4
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DOI: https://doi.org/10.1007/s00284-023-03541-4