Lactobacillus salitolerans sp. Nov., a novel lactic acid bacterium isolated from spent mushroom substrates

International Journal of Systematic and Evolutionary Microbiology

Volumn 69, Issue 4, 2019, Pages 964-969

  Tohno, Masanori ^a   Tanizawa, Yasuhiro ^b   Kojima, Yoichiro ^a   Sakamoto, Mitsuo ^c,d   Nakamura, Yasukazu ^b   Ohkuma, Moriya ^c   Kobayashi, Hisami ^a  

^a FOOD RESEARCH INSTITUTE   (Japan)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

^c RIKEN BIORESOURCE CENTER   (Japan)

^d JAPAN AGENCY FOR MEDICAL RESEARCH AND DEVELOPMENT   (Japan)

Author keywords

Lactobacillus salitolerans sp; Nov; Spent mushroom substrates

Indexed keywords

CATALASE; FATTY ACID; GENOMIC DNA; NUCLEOTIDE; RNA 16S; BACTERIAL DNA;

ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM ISOLATE; CHEMOTAXONOMY; DNA BASE COMPOSITION; GENE SEQUENCE; GRAM POSITIVE BACTERIUM; HOUSEKEEPING GENE; JAPAN; LACTIC ACID BACTERIUM; LACTOBACILLUS; LACTOBACILLUS ACIDIPISCIS; LACTOBACILLUS ACIDOPHILUS; LACTOBACILLUS POBUZIHII; LACTOBACILLUS SALITOLERANS; LACTOBACILLUS SALIVARIUS; MULTILOCUS SEQUENCE TYPING; MUSHROOM; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHS GENE; PHYLOGENETIC TREE; PRIORITY JOURNAL; RPOA GENE; AGARICALES; BACTERIUM IDENTIFICATION; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; PHYLOGENY;

AGARICALES; BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; DNA, BACTERIAL; FATTY ACIDS; JAPAN; LACTOBACILLUS; MULTILOCUS SEQUENCE TYPING; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 85064239909     PISSN: 14665026     EISSN: 14665034     Source Type: Journal    
DOI: 10.1099/ijsem.0.003224     Document Type: Article

References (40)

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.
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.
3. Mcfrederick QS, Vuong HQ, Rothman JA. Lactobacillus micheneri sp. nov., Lactobacillus timberlakei sp. nov., and Lactobacillus que-nuiae sp. nov., lactic acid bacteria isolated from wild bees and flowers. Int J Syst Evol Microbiol 2018;68:1879–1884.
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.
5. Chiou TY, Suda W, Oshima K, Hattori M, Matsuzaki C et al. Lactobacillus kosoi sp. nov., a fructophilic species isolated from k^oso, a Japanese sugar-vegetable fermented beverage. Antonie van Leeuwenhoek 2018;111:1149–1156.
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.
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.
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.
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.
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.
11. Phan CW, Sabaratnam V. Potential uses of spent mushroom substrate and its associated lignocellulosic enzymes. Appl Microbiol Biotechnol 2012;96:863–873.
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 sat-iva) cultivation: Growth promotion and soil bioremediation. Bioresour Technol 2009;100:4750–4757.
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. japon-ica) silage. FEMS Microbiol Lett 2012;337:112–119.
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.
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.
16. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBio-Cloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617.
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.
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.
19. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425.
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.
21. Hurvich CM, Tsai C-L, Regression TCL. Regression and time series model selection in small samples. Biometrika 1989;76:297– 307.
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.
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.
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.
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.
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.
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.
28. Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 2018;34:1037–1039.
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.
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.
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.
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.
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.
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.
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.
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.
37. Komagata K. Lipid SK and cell-wall analysis in bacterial systematics. Method Microbiol 1987;19:161–207.
38. Minamida K, Ota K, Nishimukai M, Tanaka M, Abe A et al. Asac-charobacter celatus gen. nov., sp. nov., isolated from rat caecum. Int J Syst Evol Microbiol 2008;58:1238–1240.
39. Chen YS, Miyashita M, Suzuki K, Sato H, Hsu JS et al. Lactobacillus pobuzihii sp. nov., isolated from pobuzihi (fermented cumming-cordia). Int J Syst Evol Microbiol 2010;60:1914–1917.
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.