Abstract
A novel Gram-stain-positive, obligately anaerobic, spore-forming rod, designated strain ChDC B114T, was isolated from a human dental plaque of a gingivitis lesion. The strain was characterized by polyphasic taxonomic analysis to identify it at the species level. The 16S ribosomal RNA gene (16S rDNA) sequence analysis revealed that the strain belongs to the genus Lachnoanaerobaculum. The percent similarity of the 16S rDNA of the strain was closest to the homologous gene sequence of Lachnoanaerobaculum orale N1T (98.5%) and Lachnoanaerobaculum saburreum CCUG 28089T (97.6%). The major fatty acids of strain ChDC B114T were C16:0 (30.7%), C14:0 (17.7%), iso-C19:0 (14.9%), and C17:0 2OH (12.0%). The draft genome of strain ChDC B114T was 3,097,953 bp in length. The G+C content of the strain was 35.9 mol %. Average nucleotide identity values between strain ChDC B114T and L. orale N1T and L. saburreum CCUG 28089T were 83.2% and 82.0%, respectively. Genome-to-genome distance values between strain ChDC B114T and L. orale N1T and L. saburreum CCUG 28089T were 26.8% (24.5–29.3%) and 26.30% (24.0–28.8%), respectively. Based on these results, strain ChDC B114T (= KCOM 2030T = JCM 33452T) should be classified as a novel species of genus Lachnoanaerobaculum, for which the name Lachnoanaerobaculum gingivalis sp. nov. is proposed.
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Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477
Cho E, Park SN, Lim YK, Shin Y, Paek J, Hwang CH, Chang YH, Kook JK (2015) Fusobacterium hwasookii sp. nov., isolated from a human periodontitis lesion. Curr Microbiol 70:169–175. https://doi.org/10.1007/s00284-014-0692-7
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
Hedberg ME, Moore ER, Svensson-Stadler L, Hörstedt P, Baranov V, Hernell O, Wai SN, Hammarström S, Hammarström ML (2012) Lachnoanaerobaculum gen. nov., a new genus in the Lachnospiraceae: characterization of Lachnoanaerobaculum umeaense gen. nov., sp. nov., isolated from the human small intestine, and Lachnoanaerobaculum orale sp. nov., isolated from saliva, and reclassification of Eubacterium saburreum (Prevot 1966) Holdeman and Moore 1970 as Lachnoanaerobaculum saburreum comb. nov. Int J Syst Evol Microbiol 62:2685–2690. https://doi.org/10.1099/ijs.0.033613-0
Jo E, Park SN, Lim YK, Paek J, Shin Y, Kim H, Kim SH, Shin JH, Chang YH, Kook JK (2018) Capnocytophaga endodontalis sp. nov., isolated from a human refractory periapical abscess. Curr Microbiol 75:420–425. https://doi.org/10.1007/s00284-017-1397-5
Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, Yabana M, Harada M, Nagayasu E, Maruyama H, Kohara Y, Fujiyama A, Hayashi T, Itoh T (2014) Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res 24:1384–1395. https://doi.org/10.1101/gr.170720.113
Kim HS, Lee DS, Chang YH, Kim MJ, Koh S, Kim J, Seong JH, Song SK, Shin HS, Son JB, Jung MY, Park SN, Yoo SY, Cho KW, Kim DK, Moon S, Kim D, Choi Y, Kim BO, Jang HS, Kim CS, Kim C, Choe SJ, Kook JK (2010) Application of rpoB and zinc protease gene for use in molecular discrimination of Fusobacterium nucleatum subspecies. J Clin Microbiol 48:545–553. https://doi.org/10.1128/JCM.01631-09
Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120
Lee I, Kim YO, 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
Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1:18. Erratum in: Gigascience (2015) 4:30
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60. https://doi.org/10.1186/1471-2105-14-60
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Sassone LM, Fidel RA, Faveri M, Figueiredo L, Fidel SR, Feres M (2012) A microbiological profile of unexposed and exposed pulp space of primary endodontic infections by checkerboard DNA-DNA hybridization. J Endod 38:889–893. https://doi.org/10.1016/j.joen.2012.03.021
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729. https://doi.org/10.1093/molbev/mst197
Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. https://doi.org/10.1093/nar/gkw569
Acknowledgments
This research was supported by the Bio & Medical Technology Development Program of the National Research Foundation (NRF) funded by the Ministry of Science and ICT (2017M3A9B8065844), in part by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (2018R1A2B5002239), and in part the KRIBB Research Initiative Program funded by the Ministry of Science, ICT and Future Planning.
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DPD number: TA00879
GenBank accession number of the 16S rRNA gene for strain ChDC B114T: MK751703
GenBank accession number of the genome for strain ChDC B114T: RRCO00000000
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284_2019_1747_MOESM2_ESM.pptx
Supplementary Material 2 (PPTX 1611 kb). Supplementary Fig S1. Maximum likelihood (A) and the minimum evolution (B) phylogenetic tree based on 16S ribosomal RNA genes of strain ChDC B114T and type strains of closely related species. The GenBank accession number of 16S rDNA of each type strain is written in parenthesis. Stability of the phylogenetic trees was assessed by the bootstrap analysis of 1,000 replicates [3] with MEGA version 6.06 [14]. Bars indicate 0.02 (A) or 0.02 (B) changes per nucleotide position. Supplementary Fig S2. Light microscope image of strain ChDC B114T for detecting the presence of spores using malachite green staining method. The stain was cultured in Brucella broth at 37°C for five days in anaerobic condition. Original magnification: 1,000. Bar = 30 μm.
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Lim, Y.K., Park, SN., Jo, E. et al. Lachnoanaerobaculum gingivalis sp. nov., Isolated from Human Subgingival Dental Plaque of a Gingivitis Lesion. Curr Microbiol 76, 1147–1151 (2019). https://doi.org/10.1007/s00284-019-01747-z
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DOI: https://doi.org/10.1007/s00284-019-01747-z