1887

Abstract

A taxonomic study of a Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, catalase-negative bacterium, strain YK43, isolated from spent mushroom substrates stored in Nagano, Japan was performed. Growth was detected at 15–45 °C, pH 5.0–8.5, and 0–10 % (w/v) NaCl. The genomic DNA G+C content of strain YK43 was 43.6 mol%. The predominant fatty acids were C, C ω9 and summed feature 8. Based on 16S rRNA gene sequence analysis, the type strains of (sequence similarity, 97.6 %) and (97.4 %) were most closely related to YK43. The average nucleotide identities were 74.1 % between strain YK43 and DSM 15836 and 74.0 % between YK43 and E100301. Based on a multilocus sequence analysis, comparative genomic analysis and a range of phenotypic and chemotaxonomic characteristics, strain YK43 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is YK43 (=JCM 31331 = DSM 103433).

Funding
This study was supported by the:
  • NARO Gender Equality Program
  • NARO Gender Equality Program
  • Japan Society for the Promotion of Science (Award 15H05897, 16H06279, 17K19248)
  • NIG JOINT (Award 2016, 2017)
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2019-01-10
2024-04-26
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References

  1. Hammes WP, Hertel C, Lactobacillus G. In Bergey’s Manual of Systematic Bacteriology, 2nd ed. vol. 3: New York: Springer; 2009 pp. pp 465–511
    [Google Scholar]
  2. Chen YS, Wang LT, Liao YJ, Lan YS, Chang CH et al. Lactobacillus musae sp. nov., a novel lactic acid bacterium isolated from banana fruits. Int J Syst Evol Microbiol 2017; 67:5144–5149 [View Article][PubMed]
    [Google Scholar]
  3. Mcfrederick QS, Vuong HQ, Rothman JA. Lactobacillus micheneri sp. nov., Lactobacillus timberlakei sp. nov., and Lactobacillus quenuiae sp. nov., lactic acid bacteria isolated from wild bees and flowers. Int J Syst Evol Microbiol 2018; 68:1879–1884 [View Article][PubMed]
    [Google Scholar]
  4. Techo S, Miyashita M, Shibata C, Tanaka N, Wisetkhan P et al. Lactobacillus ixorae sp. nov., isolated from a flower (West-Indian jasmine). Int J Syst Evol Microbiol 2016; 66:5500–5505 [View Article][PubMed]
    [Google Scholar]
  5. Chiou TY, Suda W, Oshima K, Hattori M, Matsuzaki C et al. Lactobacillus kosoi sp. nov., a fructophilic species isolated from kôso, a Japanese sugar-vegetable fermented beverage. Antonie van Leeuwenhoek 2018; 111:1149–1156 [View Article][PubMed]
    [Google Scholar]
  6. Jung MY, Lee SH, Lee M, Song JH, Chang JY et al. isolated from scallion kimchi. Int J Syst Evol Microbiol 2017; 67:4936–4942
    [Google Scholar]
  7. Tohno M, Tanizawa Y, Irisawa T, Masuda T, Sakamoto M et al. Lactobacillus silagincola sp. nov. and Lactobacillus pentosiphilus sp. nov., isolated from silage. Int J Syst Evol Microbiol 2017; 67:3639–3644 [View Article][PubMed]
    [Google Scholar]
  8. Tohno M, Kitahara M, Irisawa T, Ohmori H, Masuda T et al. Lactobacillus mixtipabuli sp. nov. isolated from total mixed ration silage. Int J Syst Evol Microbiol 2015; 65:1981–1985 [View Article][PubMed]
    [Google Scholar]
  9. Yoshida S, Mitani H, Kamata M, Ohtsuka A, Otomaru K et al. Effect of dietary fermented mushroom bed on egg production in laying hens. Biosci Biotechnol Biochem 2017; 81:2204–2208 [View Article][PubMed]
    [Google Scholar]
  10. Kim YI, Lee YH, Kim KH, Oh YK, Moon YH et al. Effects of supplementing microbially-fermented spent mushroom substrates on growth performance and carcass characteristics of Hanwoo Steers (a field study). Asian-Australas J Anim Sci 2012; 25:1575–1581 [View Article][PubMed]
    [Google Scholar]
  11. Phan CW, Sabaratnam V. Potential uses of spent mushroom substrate and its associated lignocellulosic enzymes. Appl Microbiol Biotechnol 2012; 96:863–873 [View Article][PubMed]
    [Google Scholar]
  12. Ribas LC, de Mendonça MM, Camelini CM, Soares CH. Use of spent mushroom substrates from Agaricus subrufescens (syn. A. blazei, A. brasiliensis) and Lentinula edodes productions in the enrichment of a soil-based potting media for lettuce (Lactuca sativa) cultivation: Growth promotion and soil bioremediation. Bioresour Technol 2009; 100:4750–4757 [View Article][PubMed]
    [Google Scholar]
  13. Tohno M, Kobayashi H, Tajima K, Uegaki R. Strain-dependent effects of inoculation of Lactobacillus plantarum subsp. plantarum on fermentation quality of paddy rice (Oryza sativa L. subsp. japonica) silage. FEMS Microbiol Lett 2012; 337:112–119 [View Article][PubMed]
    [Google Scholar]
  14. Tohno M, Sakamoto M, Ohkuma M, Tajima K. Paenibacillus silagei sp. nov. isolated from corn silage. Int J Syst Evol Microbiol 2016; 66:3873–3877 [View Article][PubMed]
    [Google Scholar]
  15. Kobayashi H, Nakasato T, Sakamoto M, Ohtani Y, Terada F et al. Clostridium pabulibutyricum sp. nov., a butyric-acid-producing organism isolated from high-moisture grass silage. Int J Syst Evol Microbiol 2017; 67:4974–4978 [View Article][PubMed]
    [Google Scholar]
  16. Yoon SH, Ha SM, 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 [View Article][PubMed]
    [Google Scholar]
  17. 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]
  18. 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]
  19. 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]
  20. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  21. Hurvich CM, Tsai C-L, Regression TCL. Regression and time series model selection in small samples. Biometrika 1989; 76:297–307 [View Article]
    [Google Scholar]
  22. Sugiura N. Further analysts of the data by akaike' s information criterion and the finite corrections. Commun Stat Theory Methods 1978; 7:13–26 [View Article]
    [Google Scholar]
  23. Tohno M, Kitahara M, Irisawa T, Inoue H, Uegaki R et al. Lactobacillus oryzae sp. nov., isolated from fermented rice grain (Oryza sativa L. subsp. japonica). Int J Syst Evol Microbiol 2013; 63:2957–2962 [View Article][PubMed]
    [Google Scholar]
  24. Naser SM, Dawyndt P, Hoste B, Gevers D, Vandemeulebroecke K et al. Identification of lactobacilli by pheS and rpoA gene sequence analyses. Int J Syst Evol Microbiol 2007; 57:2777–2789 [View Article][PubMed]
    [Google Scholar]
  25. Tanizawa Y, Tohno M, Kaminuma E, Nakamura Y, Arita M. Complete genome sequence and analysis of Lactobacillus hokkaidonensis LOOC260(T), a psychrotrophic lactic acid bacterium isolated from silage. BMC Genomics 2015; 16:240 [View Article][PubMed]
    [Google Scholar]
  26. 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]
  27. Tanizawa Y, Fujisawa T, Kaminuma E, Nakamura Y, Arita M. DFAST and DAGA: web-based integrated genome annotation tools and resources. Biosci Microbiota Food Health 2016; 35:173–184 [View Article][PubMed]
    [Google Scholar]
  28. 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]
  29. 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]
  30. Cai Y, Pang H, Kitahara M, Ohkuma M. Lactobacillus nasuensis sp. nov., a lactic acid bacterium isolated from silage, and emended description of the genus Lactobacillus . Int J Syst Evol Microbiol 2012; 62:1140–1144 [View Article][PubMed]
    [Google Scholar]
  31. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  32. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
    [Google Scholar]
  33. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  34. Tohno M, Kitahara M, Inoue H, Uegaki R, Irisawa T et al. Weissella oryzae sp. nov., isolated from fermented rice grains. Int J Syst Evol Microbiol 2013; 63:1417–1420 [View Article][PubMed]
    [Google Scholar]
  35. Tohno M, Kitahara M, Uegaki R, Irisawa T, Ohkuma M et al. Lactobacillus hokkaidonensis sp. nov., isolated from subarctic timothy grass (Phleum pratense L.) silage. Int J Syst Evol Microbiol 2013; 63:2526–2531 [View Article][PubMed]
    [Google Scholar]
  36. Sakamoto M, Suzuki M, Umeda M, Ishikawa I, Benno Y. Reclassification of bacteroides forsythus (Tanner et al. 1986) as Tannerella forsythensis corrig., gen. nov., comb. nov. Int J Syst Evol Microbiol 2002; 52:841–849 [View Article][PubMed]
    [Google Scholar]
  37. Komagata K. Lipid SK and cell-wall analysis in bacterial systematics. Method Microbiol 1987; 19:161–207
    [Google Scholar]
  38. 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 Microbiol 2008; 58:1238–1240 [View Article][PubMed]
    [Google Scholar]
  39. Chen YS, Miyashita M, Suzuki K, Sato H, Hsu JS et al. Lactobacillus pobuzihii sp. nov., isolated from pobuzihi (fermented cummingcordia). Int J Syst Evol Microbiol 2010; 60:1914–1917 [View Article][PubMed]
    [Google Scholar]
  40. Tanasupawat S, Shida O, Okada S, Komagata K. Lactobacillus acidipiscis sp. nov. and Weissella thailandensis sp. nov., isolated from fermented fish in Thailand. Int J Syst Evol Microbiol 2000; 50:1479–1485 [View Article][PubMed]
    [Google Scholar]
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