研究凝结芽胞杆菌(Bacillus coagulans)的分类学变迁,凝结芽胞杆菌(Bacillus coagulans)曾重新分类为凝结魏茨曼氏菌(Weizmannia coagulans),当前分类正确名称为凝结海恩德里克斯氏菌(Heyndrickxia coagulans)。该研究通过基于全基因组的分类,除了重新复核菌株CICC 20138的16S rRNA基因序列分析外,还包括核心基因组多位点序列分型(core genome multilocus sequence typing, cgMLST)、平均核苷酸一致性(average nucleotide identity, ANI)以及数字DNA-DNA杂交(digital DNA-DNA hybridization, dDDH)的种水平分析。通过形态学和生理生化特征分析获得CICC 20138的表型信息。依据16S rRNA基因序列相似性分析,CICC 20138与H.coagulans和H.faecalis的相似性最高,均为99.20%。菌株CICC 20138(GCA_009936615.1)基因组大小为3 386 433 bp,含有216个contigs,基因组DNA G+C含量为46.7 mol%。cgMLST分析结果显示,菌株CICC 20138与H.coagulans以100%支持率聚在同一分支,亲缘关系最近。ANI分析显示,CICC 20138与H.coagulans ATCC 7050T(GCA_000832905.1)的ANI值为98.16%,dDDH值为87.1%,可将CICC 20138鉴定为H.coagulans。基于全基因组序列的ANI和dDDH分析是准确有效的菌种鉴定方法,从而得到更精准的物种分类信息。对于具有潜在重要价值的菌种,全基因组序列分析是了解微生物在分类和鉴定过程中进化的重要工具。
This paper studied taxonomic changes of Bacillus coagulans, previously reclassified as Weizmannia coagulans, which currently correct name is Heyndrickxia coagulans.The study was investigated by a genome-based taxonomic classification that included, in addition to re-evaluation of the 16S rRNA gene sequence of CICC 20138, determination of core genome multilocus sequence typing (cgMLST), average nucleotide identity (ANI), and digital DNA-DNA hybridization (dDDH) analysis to species level.The phenotypic information of CICC 20138 was obtained by morphological, physiological, and biochemical analysis.Based on the analysis for the similarities of 16S rRNA gene sequences, the highest similarity to Heyndrickxia coagulans and Heyndrickxia faecalis was 99.20%.The genome size of CICC 20138 (GCA_009936615.1) was 3 386 433 bp, containing 216 contigs, and the genomic DNA G+C content was 46.7 mol%.The cgMLST analysis showed the closest genetic relationship between CICC 20138 and Heyndrickxia coagulans clustered on the same branch with 100% support.The ANI value of CICC 20138 and Heyndrickxia coagulans ATCC 7050T(GCA_000832905.1) was 98.16%, and the dDDH value was 87.1%.CICC 20138 could be identified as Heyndrickxia coagulans.ANI and dDDH analysis based on whole genome sequence should be an accurate and effective method for bacterial identification, thereby obtaining more accurate species classification information.For strains with potential significant value, whole genome sequence analysis is an important tool for understanding microbial evolution throughout classification and identification.
[1] HAMMER B W.Bacteriological studies on the coagulation of evaporated milk[J].Iowa Agricultural Experimental Station Research Bulletin, 1915, 19:119-131.
[2] SKERMAN V B D, MCGOWAN V,SNEATH P H A. Approved lists of bacterial names. International Journal of Systematic and Evolutionary Microbiology, 1980, 30(1):225-420.
[3] CLERCK E D, RODRIGUEZ-DIAZ M, FORSYTH G, et al.Polyphasic characterization of Bacillus coagulans strains, illustrating heterogeneity within this species, and emended description of the species[J].Systematic & Applied Microbiology, 2004, 27(1):50-60.
[4] GUPTA R S, PATEL S, SAINI N, et al.Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses:description of Robertmurraya kyonggiensis sp.nov.and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species[J].International Journal of Systematic and Evolutionary Microbiology, 2020, 70(11):5753-5798.
[5] RAO M P N, BANERJEE A, LIU G H, et al.Genome-based reclassification of Bacillus acidicola, Bacillus pervagus and the genera Heyndrickxia, Margalitia and Weizmannia[J].International Journal of Systematic and Evolutionary Microbiology, 2023, 73(7):5961.
[6] WHITMAN W B, VOS P D, GARRITY G M, et al.Bergey's Manual of Systematic Bacteriology Second Edition[M].New York:Springer Science, 2009.
[7] KONURAY G, ERGINKAYA Z.Potential use of Bacillus coagulans in the food industry[J].Foods, 2018, 7(6):92.
[8] ZHOU Y H, ZENG Z H, XU Y B, et al.Application of Bacillus coagulans in animal husbandry and its underlying mechanisms[J].Animals (Basel), 2020, 10(3):454.
[9] MU Y, CONG Y.Bacillus coagulans and its applications in medicine[J].Beneficial Microbes, 2019, 10(6):679-688.
[10] JUTURU V, WU J C.Microbial production of lactic acid:The latest development[J].Critical Reviews in Biotechnology, 2016, 36(6):967-977.
[11] FU R Q, CHEN D W, TIAN G, et al.Effect of dietary supplementation of Bacillus coagulans or yeast hydrolysates on growth performance, antioxidant activity, cytokines and intestinal microflora of growing-finishing pigs[J].Animal Nutrition, 2019, 5(4):366-372.
[12] 王一帆, 岑丛楠, 刘福奇, 等.凝结芽孢杆菌的益生特性及机制研究进展[J].食品工业科技, 2023, 44(1):458-464.
WANG Y F, CEN C N, LIU F Q, et al.Research progress on the probiotic characteristics and mechanism of Bacillus coagulans[J].Science and Technology of Food Industry, 2023, 44(1):458-464.
[13] STECKER R A, MOON J M, RUSSO T J, et al.Bacillus coagulans GBI-30, 6086 improves amino acid absorption from milk protein[J].Nutrition & Metabolism, 2020, 17:93.
[14] MAITY C, GUPTA P A K, SAROJ D B, et al.Impact of a gastrointestinal stable probiotic supplement Bacillus coagulans LBSC on human gut microbiome modulation[J].Journal of Dietary Supplements, 2021, 18(6):577-596.
[15] KUMAR S, STECHER G, LI M, et al.MEGA X:Molecular evolutionary genetics analysis across computing platforms[J].Molecular Biology and Evolution, 2018, 35(6):1547-1549.
[16] PARKS D H, IMELFORT M, SKENNERTON C T, et al.CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes[J].Genome Research, 2015, 25(7):1043-1055.
[17] DELCHER A L, BRATKE K A, POWERS E C, et al.Identifying bacterial genes and endosymbiont DNA with Glimmer[J].Bioinformatics, 2007, 23(6):673-679.
[18] FU L M, NIU B F, ZHU Z W, et al.CD-HIT:Accelerated for clustering the next-generation sequencing data[J].Bioinformatics, 2012, 28(23):3150-3152.
[19] KIM M, OH H S, PARK S C, et al.Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes[J].International Journal of Systematic and Evolutionary Microbiology, 2014, 64(Pt 2):346-351.
[20] MEIER-KOLTHOFF J P, CARBASSE J S, PEINADO-OLARTE R L, et al.TYGS and LPSN:A database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes[J].Nucleic Acids Research, 2022, 50(D1):D801-D807.
[21] THOMPSON C C, CHIMETTO L, EDWARDS R A, et al.Microbial genomic taxonomy[J].BMC Genomics, 2013, 14:913.
[22] BANOON S R, ALI Z M.Identification the local thermophilic strains of Bacillus licheniformis by VITEK-2 system and Gyrase B gene[J].Al-Kufa University Journal for Biology, 2018, 10(2):47-57.
[23] 杨晶, 王伟欢.VITEK 2 Compact系统的应用及鉴定结果分析[J].中国卫生检验杂志, 2016, 26(18):2643-2645.
YANG J, WANG W H.Application of VITEK 2 Compact system and its identification results analysis[J].Chinese Journal of Health Laboratory Technology, 2016, 26(18):2 643-2 645.
[24] HUANG C H, CHEN C C, LIOU J S, et al.Genome-based reclassification of Lactobacillus casei:Emended classification and description of the species Lactobacillus zeae[J].International Journal of Systematic and Evolutionary Microbiology, 2020, 70(6):3755-3762.
