1887

Abstract

During a study on the biodiversity of bacteria that inhabit woody biomass, we isolated a strain coded B40 from hardwood bark used as a compost ingredient in Japan. The strain, characterized as B40, is a Gram-stain-positive, rod-shaped, non-motile, non-spore-forming and catalase-negative bacterium. This novel isolate showed growth at 30–50 °C, at pH 3.5–7.5 and in the presence of up to 4 % (w/v) NaCl. Its major fatty acids include C, C ω and summed feature 8. The genomic DNA G+C content of strain B40 is 42.2 mol%. Results of 16S rRNA gene sequence-based phylogenetic analysis indicated that strain B40 belongs to the genus and the closest neighbours of strain B40 are 202 (95.7 %), CRBIP 24.76 (95.6 %), DSM 15354 (95.4 %), TV1018 (95.4 %) and ATCC 25258 (95.2 %). The amino acid sequence-based phylogenetic analyses of 489 shared protein-encoding genes showed that the strain forms a phylogenetically independent lineage in the genus but could not be assigned to any known species. Strain B40 has an average nucleotide identify of <70.2 % and a digital DNA–DNA hybridization value of 19.2 % compared with the strains of other closely related species. Differential genomic, phenotypic and chemotaxonomic properties, in addition to phylogenetic analyses, indicated that strain B40 represents a novel species of the genus , for which the name sp. nov. is proposed. The strain type is B40 (=JCM 32597=DSM 107967).

Funding
This study was supported by the:
  • NARO and NIG JOINT (2016, 2017)
    • Principle Award Recipient: MasanoriTohno
  • NARO Gender Equality Program, Genebank Project (Microorganism Section)
    • Principle Award Recipient: HisamiKobayashi
  • NARO Gender Equality Program, Genebank Project (Microorganism Section)
    • Principle Award Recipient: MasanoriTohno
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2021-07-15
2021-07-29
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References

  1. Beijerinck MW. Sur les ferments lactiques de l’industrie [Production of lactic ferments in the dairy industry]. Archiv Neerlandaises des Sciences Exactes et Naturelles 1901; 6:212–243
    [Google Scholar]
  2. Hammes WP, Hertel C. Genus Lactobacillus. In In Bergey’s Manual of systematic Bacteriology, 2nd. edn New York: Springer; 2009 pp 465–511
    [Google Scholar]
  3. Zheng J, Wittouck S, Salvetti E, Franz C, Harris HMB et al. 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 2020; 70:2782–2858 [View Article] [PubMed]
    [Google Scholar]
  4. Fujisawa T, Benno Y, Yaeshima T, Mitsuoka T. Taxonomic study of the Lactobacillus acidophilus group, with recognition of Lactobacillus gallinarum sp. nov. and Lactobacillus johnsonii sp. nov. and synonymy of Lactobacillus acidophilus group A3 (Johnson et al. 1980) with the type strain of Lactobacillus amylovorus (Nakamura 1981. Int J Syst Bacteriol 1992; 42:487–491 [View Article] [PubMed]
    [Google Scholar]
  5. Cousin S, Motreff L, Gulat-Okalla ML, Gouyette C, Spröer C et al. Lactobacillus pasteurii sp. nov. and Lactobacillus hominis sp. nov. Int J Syst Evol Microbiol 2013; 63:53–59 [View Article]
    [Google Scholar]
  6. Roos S, Engstrand L, Jonsson H. Lactobacillus gastricus sp. nov., Lactobacillus antri sp. nov., Lactobacillus kalixensis sp. nov. and Lactobacillus ultunensis sp. nov., isolated from human stomach mucosa. Int J Syst Evol Microbiol 2005; 55:77–82 [View Article] [PubMed]
    [Google Scholar]
  7. Gasser F, Mandel M, Rogosa M. Lactobacillus jensenii sp.nov., a new representative of the subgenus Thermobacterium. J Gen Microbiol 1970; 62:219–222 [View Article] [PubMed]
    [Google Scholar]
  8. Dicks LM, Silvester M, Lawson PA, Collins MD. Lactobacillus fornicalis sp. nov., isolated from the posterior fornix of the human vagina. Int J Syst Evol Microbiol 2000; 50:1253–1258 [View Article]
    [Google Scholar]
  9. Falsen E, Pascual C, Sjoden B, Ohlen M, Collins MD. Phenotypic and phylogenetic characterization of a novel Lactobacillus species from human sources: description of Lactobacillus iners sp. nov. Int J Syst Bacteriol 1999; 49:217–221
    [Google Scholar]
  10. Rocha J, Botelho J, Ksiezarek M, Perovic SU, Machado M et al. Lactobacillus mulieris sp. nov., a new species of Lactobacillus delbrueckii group. Int J Syst Evol Microbiol 2020; 70:1522–1527 [View Article] [PubMed]
    [Google Scholar]
  11. Lauer E, Kandler O. Lactobacillus gasseri sp. nov., a new species of the subgenus Thermobacterium. Zentralbl Bakteriol Parasitenkd Infektionskr Hyg Abt 1 Orig Reihe C 1980; 1:75–78
    [Google Scholar]
  12. Hansen PA, Mocquot G. Lactobacillus acidophilus (Moro) comb. nov. Int J Syst Bacteriol 1970; 20:325–327 [View Article]
    [Google Scholar]
  13. Tanizawa Y, Tada I, Kobayashi H, Endo A, Maeno S et al. Lactobacillus paragasseri sp. nov., a sister taxon of Lactobacillus gasseri, based on whole-genome sequence analyses. Int J Syst Evol Microbiol 2018; 68:3512–3517 [View Article] [PubMed]
    [Google Scholar]
  14. Zhang S, Yang M, Su H, Rollins D, Zhang S. Lactobacillus colini sp. nov., isolated from Northern Bobwhite (Colinus virginianus. Int J Syst Evol Microbiol 2017; 67:325–329 [View Article] [PubMed]
    [Google Scholar]
  15. Morita H, Shimazu M, Shiono H, Toh H, Nakajima F et al. Lactobacillus equicursoris sp. nov., isolated from the faeces of a thoroughbred racehorse. Int J Syst Evol Microbiol 2010; 60:109–112 [View Article] [PubMed]
    [Google Scholar]
  16. Cousin S, Gulat-Okalla ML, Motreff L, Gouyette C, Bouchier C et al. Lactobacillus gigeriorum sp. nov., isolated from chicken crop. Int J Syst Evol Microbiol 2012; 62:330–334 [View Article] [PubMed]
    [Google Scholar]
  17. Mukai T, Arihara K, Ikeda A, Nomura K, Suzuki F et al. Lactobacillus kitasatonis sp. nov., from chicken intestine. Int J Syst Evol Microbiol 2003; 53:2055–2059 [View Article] [PubMed]
    [Google Scholar]
  18. Mitsuoka T, Fujisawa T. Lactobacillus hamsteri, a new species from the intestine of hamsters. Proc Jpn Acad Ser B Phys Biol Sci 1987; 63:269–272 [View Article]
    [Google Scholar]
  19. Fujisawa T, Itoh K, Benno Y, Mitsuoka T. Lactobacillus intestinalis (ex Hemme 1974) sp. nov., nom. rev., isolated from the intestines of mice and rats. Int J Syst Bacteriol 1990; 40:302–304 [View Article] [PubMed]
    [Google Scholar]
  20. Kim JS, Choe H, Kim KM, Lee YR, Rhee MS et al. Lactobacillus porci sp. nov., isolated from small intestine of a swine. Int J Syst Evol Microbiol 2018; 68:3118–3124 [View Article] [PubMed]
    [Google Scholar]
  21. Lawson PA, Wacher C, Hansson I, Falsen E, Collins MD. Lactobacillus psittaci sp. nov., isolated from a hyacinth macaw (Anodorhynchus hyacinthinus. Int J Syst Evol Microbiol 2001; 51:967–970 [View Article] [PubMed]
    [Google Scholar]
  22. Killer J, Havlik J, Vlkova E, Rada V, Pechar R et al. Lactobacillus rodentium sp. nov., from the digestive tract of wild rodents. Int J Syst Evol Microbiol 2014; 64:1526–1533 [View Article] [PubMed]
    [Google Scholar]
  23. Meng J, Jin D, Yang J, Lai XH, Pu J et al. Lactobacillus xujianguonis sp. nov., isolated from faeces of Marmota himalayana. Int J Syst Evol Microbiol 2020; 70:11–15 [View Article] [PubMed]
    [Google Scholar]
  24. Entani E, Masai H, Suzuki K. Lactobacillus acetotolerans, a new species from fermented vinegar broth. Int J Syst Bacteriol 1986; 36:544–549 [View Article]
    [Google Scholar]
  25. Bohak I, Back W, Richter L, Ehrmann M, Ludwig W et al. Lactobacillus amylolyticus sp. nov., isolated from beer malt and beer wort. Syst Appl Microbiol 1998; 21:360–364 [View Article] [PubMed]
    [Google Scholar]
  26. Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM. Bergey’s Manual of Determinative Bacteriology, 2nd ed. Baltimore: The Williams & Wilkins Co; 1925
    [Google Scholar]
  27. Fujisawa T, Adachi S, Toba T, Arihara K, Mitsuoka T. Lactobacillus kefiranofaciens sp. nov. isolated from kefir grains. Int J Syst Bacteriol 1988; 38:12–14 [View Article]
    [Google Scholar]
  28. Wang LT, Kuo HP, Wu YC, Tai CJ, Lee FL. Lactobacillus taiwanensis sp. nov., isolated from silage. Int J Syst Evol Microbiol 2009; 59:2064–2068
    [Google Scholar]
  29. Nakamura LK. Lactobacillus amylovorus, a new starch-hydrolyzing species from cattle waste-corn fermentations. Int J Syst Bacteriol 1981; 31:56–63 [View Article]
    [Google Scholar]
  30. Killer J, Dubna S, Sedlacek I, Svec P. Lactobacillus apis sp. nov., from the stomach of honeybees (Apis mellifera), having an in vitro inhibitory effect on the causative agents of American and European foulbrood. Int J Syst Evol Microbiol 2014; 64:152–157 [View Article] [PubMed]
    [Google Scholar]
  31. Praet J, Meeus I, Cnockaert M, Houf K, Smagghe G et al. Novel lactic acid bacteria isolated from the bumble bee gut: Convivina intestini gen. nov., sp. nov., Lactobacillus bombicola sp. nov., and Weissella bombi sp. nov. Antonie van Leeuwenhoek 2015; 107:1337–1349 [View Article] [PubMed]
    [Google Scholar]
  32. Olofsson TC, Alsterfjord M, Nilson B, Butler E, Vasquez A. Lactobacillus apinorum sp. nov., Lactobacillus mellifer sp. nov., Lactobacillus mellis sp. nov., Lactobacillus melliventris sp. nov., Lactobacillus kimbladii sp. nov., Lactobacillus helsingborgensis sp. nov. and Lactobacillus kullabergensis sp. nov., isolated from the honey stomach of the honeybee Apis mellifera. Int J Syst Evol Microbiol 2014; 64:3109–3119 [View Article] [PubMed]
    [Google Scholar]
  33. Wang C, Huang Y, Li L, Guo J, Wu Z et al. Lactobacillus panisapium sp. nov., from honeybee Apis cerana bee bread. Int J Syst Evol Microbiol 2018; 68:703–708 [View Article] [PubMed]
    [Google Scholar]
  34. Tohno M, Kobayashi H, Nomura M, Kitahara M, Ohkuma M et al. Genotypic and phenotypic characterization of lactic acid bacteria isolated from Italian ryegrass silage. Anim Sci J 2012; 83:111–120 [View Article] [PubMed]
    [Google Scholar]
  35. Tanizawa Y, Kobayashi H, Nomura M, Sakamoto M, Arita M et al. Lactobacillus buchneri subsp. silagei subsp. nov., isolated from rice grain silage. Int J Syst Evol Microbiol 2020; 70:3111–3116 [View Article] [PubMed]
    [Google Scholar]
  36. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617
    [Google Scholar]
  37. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
    [Google Scholar]
  38. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
    [Google Scholar]
  39. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  40. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
    [Google Scholar]
  41. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
    [Google Scholar]
  42. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
    [Google Scholar]
  43. Hurvich CM, Tsai CL. Regression and time series model selection in small samples. Biometrika 1989; 76:297–307 [View Article]
    [Google Scholar]
  44. Sugiura N. Further analysis of data by Akaikes information criterion and finite corrections. Commun Stat a-Theor 1978; 7:13–26
    [Google Scholar]
  45. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Micr 2014; 64:1825
    [Google Scholar]
  46. Kobayashi H, Tanizawa Y, Sakamoto M, Nakamura Y, Ohkuma M. Reclassification of Paenibacillus thermophilus Zhou et al. 2013 as a later heterotypic synonym of Paenibacillus macerans (Schardinger 1905) Ash et al. 1994. Int J Syst Evol Microbiol 2019; 69:417–421 [View Article] [PubMed]
    [Google Scholar]
  47. Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y et al. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res 2014; 24:1384–1395 [View Article] [PubMed]
    [Google Scholar]
  48. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 2018; 34:i884–i890 [View Article] [PubMed]
    [Google Scholar]
  49. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  50. Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 2018; 34:1037–1039 [View Article] [PubMed]
    [Google Scholar]
  51. Cosentino S, Iwasaki W. SonicParanoid: fast, accurate and easy orthology inference. Bioinformatics 2019; 35:149–151 [View Article] [PubMed]
    [Google Scholar]
  52. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
    [Google Scholar]
  53. Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 2007; 56:564–577 [View Article] [PubMed]
    [Google Scholar]
  54. Kuck P, Longo GC. FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies. Front Zool 2014; 11:81 [View Article] [PubMed]
    [Google Scholar]
  55. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
    [Google Scholar]
  56. Richter M, Rossello-Mora R, Oliver Glockner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
    [Google Scholar]
  57. Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  58. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
  59. Tohno M, Tanizawa Y, Kojima Y, Sakamoto M, Nakamura Y et al. Lactobacillus salitolerans sp. nov., a novel lactic acid bacterium isolated from spent mushroom substrates. Int J Syst Evol Microbiol 2019; 69:964–969 [View Article] [PubMed]
    [Google Scholar]
  60. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Method Microbiol 1987; 19:161–207
    [Google Scholar]
  61. Minamida K, Ota K, Nishimukai M, Tanaka M, Abe A et al. Asaccharobacter celatus gen. nov., sp nov., isolated from rat caecum. Int J Syst Evol Micr 2008; 58:1238–1240
    [Google Scholar]
  62. Sakamoto M, Suzuki M, Umeda M, Ishikawa I, Benno Y. Reclassification of Bacteroides forsythus (Tanner et al. 1986) as Tannerella forsythensis corrig., gen. Int J Syst Evol Microbiol 2002; 52:841–849 [View Article] [PubMed]
    [Google Scholar]
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