微生物遺伝資源利用マニュアル(15)
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- しょうじ いんそん
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1 (15) MAFF Microorganism Genetic Resources Manual No.15 Lactic acid bacteria isolated from silage DNA G+C a 1994 Lactobacillus plantarum Lactobacillus casei McDonald et al Ohmomo et al Lactobacillus Leuconostoc Lactococcus, Enterococcus Pediococcus Weissella Cai et al. 1999b 1999d Zhang et al Ennahar b mm KN mm g SQ-202 1
2 g 10 g 90 ml GYP 1992 MRS gcfu/g 2001b Sample Salt solution MRS agar GYP-CaCO3 BCP agar Acetate agar days MRS
3 MRS 10 Dimethyl sulfoxide NA Bacto-Beef Extract 3 g + Bacto-Peptone 5 g/l ml MRS Lactobacillus, Streptococcus, Pediococcus, Leuconosotoc Bergey s Munual of Systematic Bacteriology Vol.2 16S RNA 1996 DNA GC 16S rrna DNA Ezaki et al ) 16S rrna Schleifer and Ludwing 1989 Woese1987 parsimony 16S rrna 2 MRS30 N-AcetylmuramidaseLysozyme DNA DNA 27F (5 -AGAGGACCGGCCAG-3 ) 1492R (5 -GGACCGA CGAC-3 ) akara aq M GeneAmp PCR System 9700 (Applied Biosystems, USA) PCR 16S rdna 1500 bppcrdna SUPREC M -02 BigDye Primer Cycle Sequencing Kit GeneAmp PCR System 9700 (Applied Biosystems, USA)Applied Biosystems DNA ABI PRISM M 310 Genetic Analyzer 16S rdnablas Homology Search Altsuchul et al DNA GemBank/EMBL/DDBJ CLUSAL Whompson et al Saitou and Nei
4 (type strain) DNA DNA Gold Standard of axonomy species 70 DNA 50 3 Species Subspecies DNA-DNA homology value Closely related independent species 4
5 DNA DNA Ezaki (1989) MRS 12 DNA DNA DNA DNA DNA DNA Streptavidin-conjugated enzyme streptavidin DNA DNA DNA-DNA MRS 12 DNA DNA DNA DNA DNA DNA streptavidin-conjugated enzyme streptavidin DNA DNA Ezaki 1989 MRS Lactococcus lactis subsp.lactis Lactobacillus plantarum 4 MAFF Leuconostoc pseudomesenteroides 1999/ Leuconostoc sp. 1999/ Leuconostoc sp. 1999/ Leuconostoc sp. 1999/ Leuconostoc sp. 1999/ Lactococcus lactis subsp. lactis 1999/ Lactococcus sp. 1999/ Lactococcus sp. 1999/ Lactococcus sp. 1999/ Lactococcus sp. 1999/ Lactococcus lactis subsp. lactis 1999/ Lactococcus sp. 1999/ Lactococcus sp. 1999/ Lactococcus sp. 1999/ Lactococcus sp. 1999/ Lactococcus sp. 1999/ Lactococcus sp. 1999/ Lactococcus sp. 1999/ Weissella confusa 1999/ Pediococcus acidilactici 1999/ Pediococcus sp. 1999/ Pediococcus sp. 1999/ Pediococcus sp. 1999/ Pediococcus sp. 1999/
6 MAFF Pediococcus sp. 1999/ Pediococcus sp. 1999/ Lactobacillus brevis 1999/ Lactobacillus sp. 1999/ Lactobacillus sp. 1999/ Pediococcus pentosaceus 1999/ Enterococcus faecalis 1999/ Enterococcus sp. 1999/11 92a Enterococcus sp. 1999/11 92b Lactobacillus rhamnosus 1999/ Lactobacillus sp. 1999/ Lactobacillus sp. 1999/ Lactobacillus sp. 1999/ Lactobacillus sp. 1999/ Lactobacillus sp. 1999/ Lactobacillus sp. 1999/ Lactobacillus plantarum 1999/ Lactobacillus sp. 1999/ Lactobacillus sp. 1999/ Lactobacillus sp. 1999/ Lactobacillus sp. 1999/ Lactobacillus sp. 1999/ Lactobacillus sp. 1999/ Lactobacillus sp. 1999/ Lactobacillus sp. 1999/ Lactobacillus sp. 1999/ Lactococcus lactis subsp. lactis 2000/ Lactococcus lactis subsp. lactis 2000/ Lactococcus lactis subsp. lactis 2000/ Lactococcus lactis subsp. lactis 2000/ Pediococcus acidilactici 2000/ Pediococcus acidilactici 2000/ Pediococcus acidilactici 2000/ Lactobacillus plantarum 2000/ Lactobacillus plantarum 2000/ Lactobacillus plantarum 2000/ Lactobacillus plantarum 2000/ Lactobacillus plantarum 2000/ Lactobacillus plantarum 2000/ Enterococcus faecalis 2000/ Enterococcus faecalis 2000/ Enterococcus mundtii 2000/ Lactobacillus sakei 2000/ Pediococcus pentosaceus 2000/ Lactobacillus brevis 2000/ Lactobacillus brevis 2000/ Lactobacillus brevis 2000/ Pediococcus acidilactici 2000/ Leuconostoc citreum 2000/ Leuconostoc lactis 2000/ Lactobacillus casei 2000/ Lactobacillus ferintoshensis 2000/ Lactobacillus ferintoshensis 2000/ Leuconostoc citreum 2000/ Lactococcus lactis subsp. lactis 2000/9 2 6
7 Enterococcus gallinarum 2000/ Leuconostoc citreum 2000/ Lactobacillus plantarum 2000/ Leuconostoc citreum 2000/ Weissella paramensenteroides 2000/ Pediococcus acidilactici 2000/ Leuconostoc citreum 2000/ Lactobacillus casei 2001/9 CO Lactobacillus casei 2001/9 CO Lactobacillus casei 2001/9 CO Leuconostoc pseudomesenteroides 2001/9 CO74 ABLE 1. Phenotypic 2 characteristics of lactic acid bacteria isolated from a paddy rice silage a Groups A B C D E F G H I J Number of strains Representative strain Shape Gram stain Fermentation type Catalase Glycerol Erythritol D-Arabinose L-Arabinose Ribose D-Xylose L-Xylose Adonitol β Methyl-xyloside Galactose D-Glucose D-Fructose D-Mannose L-Sorbose Rhamnose Dulcitol Inositol Mannitol Sorbitol α Methyl-D-mannoside α Methyl-D-glucoside N acetyl glucosamine Amygdaline Arbutine Esculine Salicine Cellobiose Maltose Lactose Melibiose Saccharose rehalose Inulin Melezitose D-Raffinose Starch Glycogene Xylitol β Gentiobiose D-uranose D-Lyxose D-agatose D-Fucose L-Fucose D-Arabitol L-Arabitol Gluconate 2 ceto-gluconate RO6 RO3 RO95 RO17 RO90 RO1 RO7 RO5 RO66 RO97 Cocci Cocci Cocci Cocci Cocci Cocci Rods Rods Rods Rods Homo Homo Homo Homo Homo Hetero Homo Hetero Hetero Hetero w w w w w w w w w w w w w w w a +, positive;, negative; w, weakly positive; Homo, homofermentative; Hetero, heterofermentative. 7
8 MRS Difco 16S rrna DNA-DNA 2 10 A-J group RO3 RO6 RO95 RO17 RO90 L(+) RO1 RO5 D(-) RO7 DL RO66 RO97 DL 16S rrna RO1 Leuconostoc, RO3 RO6 Lactococcus RO17 RO95 Pediococcus RO90 Enterococcus RO7 RO66 RO97 Lactobacillus RO5 Weissella 5 6 DNAG+C DNA-DNA 3 DNA G+C DNA-DNA 85 DNA-DNA RO1 Leuconostoc pseudomesenteroides, RO3 RO6 Lactococcus lactis subsp. lactis RO17 Pediococcus pentosaceus RO95 Pediococcus pentosaceus RO90 Enterococcus faecalis RO7 Lactobacillus plantarum RO66 RO97 Lactobacillus brevis RO5 Weissella kimchii Leuconostoc Weissella D( ) D(-) Cai et al Pediococcus acidilactici Lactobacillus plantarum ph MRS ph 3.6 ph Pediococcus acidilactici 50 48Cai et al. 1999c 2001a annock 1999 Lactococcus lacti s Lactococcus lactis Pediococcus Characteristic subsp. lactis RO6 subsp. lactis RO3 pentosaceus RO95 Pediococcus acidilactici RO17 Enterococcus faecalis RO90 DNAG+C (%) DNA-DN A(%) Characteristic Leuconostoc pseudo - mensenteroides RO1 Lactobacillus plantarum RO7 Weissella confusa RO5 Lactobacillus brevis RO66 Lactobacillus brevis RO97 DNAG+C (%) DNA-DN A(%)
9 E. villorum E. mundtii E. pseudoavium E. hirae E. faecium E. durans E. raffinosus E. malodoratus E. avium E. gallinarum 99 E. flavescens E. casseliflavus 86 E. dispar E. asini E. moraviensis E. faecalis RO90 E. sulfureus E. saccharolyticus E. cecorum 95 P. dextrinicus E. columbae 97 P. urinaeequi P. parvulus P. inopinatus P. damnosus P. acidilactici RO17 P. pentosaceus RO95 E. haemoperoxidus B. subtilis E. solitarius Le. fallax 97 RO1 L. raffinolactis L. plantarum L. piscium L. lactis subsp. cremoris L. lactis subsp. lactis RO6 RO3 Le. gasicomitatum Le. carnosum Le. lactis Le. citreum Le. mesenteroides subsp. dextranicum Le. mesenteroides subsp. mesenteroides Le. mesenteroides subsp. cremoris Le. gelidum Le. pseudomesenteroides L. garvieae Le. argentinum O. Oeni IFO ( D87677) JCM 5887 ( D87679) JCM 5889 ( D88528) LMG ( AJ271329) DSM ( AJ271383) DSM ( AJ318414) DSM ( AJ305321) his study ( AF515227) DSM ( AJ305320) his study ( AF515229) LMG ( AJ301836) LMG ( AJ301837) LMG 6399 ( AJ301834) LMG ( AJ301830) DSM ( AJ276354) NCIMB ( Y18296) LMG ( AJ301835) LMG ( AJ301825) LMG ( AJ301833) LMG ( AJ301832) LMG ( AJ301826) LMG ( AJ301829) ACC ( Y11621) LMG ( AF286831) LMG ( AF286832) LMG 7937 ( AJ301831) his study ( AF515223) LMG ( AJ301841) LMG ( AJ301839) LMG ( AJ301828) LMG ( AJ301827) DSM 5634 ( AJ301840) NCDO 1769 ( X60646) his study ( AF515228) NCDO 617 ( X54261) NCDO 1869 ( X54259) ACC ( X53905) JCM 8735 ( AB012306) ACC ( M58836) ACC ( M58837) his study ( AF515224) his study ( AF515225) JCM 6125 (M35820) DSM ( S63851) LMG ( AF231131) NRIC 1722 ( AB022925) JCM 6123 ( AB023968) NRIC 1776 ( AB022923) DSM 8581 ( AF175403) NRIC 1539 ( AB023246) DSM ( M23035) DSM ( M23034) NRIC 1778 ( AB022921) NRIC 1777 ( AB023237) 5 Leuconostoc Lactococcus Pediococcus Enterococcus S RNAKnucNJ 0.02 K nuc 9
10 L. collinoides L. arizonensis 94 L. paraplantarum 61 L. plantarum L. pentosus 93 RO7 L. hilgardii L. kefiri 99 L. parabuchneri L. parakefiri L. buchneri 95 L. brevis RO66 RO97 L. kunkeei L. sanfranciscensis L. lindneri L. fructivorans L. farciminis L. paralimentarius 61 L. kimchii L. alimentarius L. sakei subsp. sakei L. curvatus L. sharpeae L. manihotivorans L. rhamnosus L. zeae 84 L. casei L. coryniformis L. bifermentans P. selangorensis L. perolens L. algidus L. nagelii L. mali L. ruminis L. murinus L. animalis 66 L. mucosae L. agilis L. salivarius subsp. salivarius L. salivarius subsp. salicinius L. aviarius subsp. aviarius L. aviarius subsp. araffinosus L. cypricasei L. acidipiscis ACC ( AB005893) JCM ( AF093757) DSM ( AJ306297) JCM 1149 ( D79210) JCM 1558 ( D79211) his study ( AF515222) DSM ( M58821) NRIC 1693 (AB024300) LMG ( AY026751) LMG ( AY026750) DSM ( M58811) ACC ( M58810) his study ( AF515220) his study ( AF515219) ACC ( Y11374) ACC ( M58830) DSM ( X95421) DSM ( X76330) ACC ( M58817) DSM ( AJ417500) JCM ( AF183558) DSM ( M58804) DSM ( M58829) DSM ( AJ270951) DSM ( M58831) LMG ( AF000162) ACC 7469 ( M58815) ACC ( D86516) ACC 334 ( D86517) DSM ( M58813) DSM ( M58809) LMG ( AF049745) DSM ( Y19167) JCM (AB033209) ACC ( Y17500) DSM ( M58824) DSM ( M58828) DSM ( M58826) DSM ( M58807) JCM ( AB048833) DSM ( M58803) ACC ( AF089108) DSM ( M59054) DSM ( M58808) JCM 5667 (AB001837) CCUG ( AJ251560) JCM (AB023836) 0.01 K nuc DSM ( AF126738) L. reuteri L. vaginalis 93 L. panis L. oris L. pontis L. frumenti L. coleohominis L. amylophilus L. johnsonii L. gasseri L. psittaci L. jensenii L. fornicalis L. helveticus W. viridescens 68 W. halotolerans W. soli W. kandleri W. thailandensis W. paramesenteroides W. hellenica W. confusa W. cibaria W. kimchii RO5 B. subtilis L. iners L. delbrueckii subsp. lactis L. delbrueckii subsp. delbrueckii L. delbrueckii subsp. bulgaricus L. intestinalis L. hamsteri L. amylolyticus L. crispatus L. amylovorus L. gallinarum L. acidophilus L. acetotolerans L. fructosus DSM ( L23507) NCC ( X61136) DSM 6035 ( X94230) DSM 4864 ( X94229) ACC ( X76329) DSM ( AJ250074) CCUG ( AJ292530) DSM ( M58806) CCUG ( Y16329) ACC ( AJ002515) DSM ( M58820) CCUG ( AJ272391) ACC ( AF243176) ACC ( Y18654) ACC ( M58823) ACC 9649 ( M58814) JCM 2 ( AB007908) DSM 6629 ( AJ306299) DSM 5661 ( AJ306298) DSM ( Y17361) DSM ( Y17362) DSM ( M58805) NCDO 2712 ( X61141) ACC ( AJ242968) ACC 4356 ( M58802) DSM ( M58801) NCDO 2345 ( X61140) DSM ( M23040) DSM ( M23037) DSM ( AY028260) DSM ( M23038) JCM ( AB023838) NCFB 803 (AB023238) NCFB 2973 ( X95981) JCM 1093 ( M23036) LMG ( AJ295989) DSM ( AF312874) his study ( AF515221) NCDO 1769 ( X60646) 6 Lactobacillus WeissellaS RNA KnucNJ 10
11 Altschul, S.F.,.F. Madden, A.A. Schaffer, J. Zhang, W. Miller and D.J. Lipman (1997) Gapped BLAS and PSI-BLAS: a new generation of protein database search programs. Nucleic Acids Res. 25: (1996) ( )... pp Cai, Y. (1999) Identification and characterization of Enterococcus species isolated from forage crops and their influence on silage fermentation. J. Dairy Sci. 82: (2001a). 47: (2001b)... pp (2002). 56: Cai, Y. and S. Kumai (1994) he proportion of lactate isomers in farm silage and the influence of inoculation with lactic acid bacteria on the proportion of L-lactate in silage. Jan. J. Zootech.l Sci. 65: Cai Y., H. Okada, H. Mori, Y. Benno and. Nakase. (1999a) Lactobacillu s paraalimentarius sp. nov. isolated from sourdough. International Journal of Systematic Bacteriology 49: (1991a). 37: (1991b). 37: (1995). 66: (1994). 39: Cai, Y., S. Kumai, J. Zhang and Y. Benno (1999b) Comparative studies of lactobacilli and enterococci associated with forage crops as silage inoculants. Anim. Sci. J. 70: Cai, Y., S. Kumai, M. Ogawa, Y. Benno and. Nakase (1999c) Characterization and Identification of Pediococcus species isolated from forage crops and their application for silage preparation. Appl. Environ. Microbiol. 65: Cai, Y., Y. Benno, M. Ogawa and S. Kumai (1999d) Effect of applying lactic acid bacteria isolated from forage crops on fermentation characteristics and aerobic deterioration of silage. J. Dairy Sci. 82: Cai, Y., Y. Benno, M. Ogawa, S. Ohmomo, S. Kumai and. Nakase (1998) Influence of Lactobacillus spp. from an inoculant and of Weissella and Leuconostoc spp. from forage crops on silage fermentation. Appl. Environ. Microbiol. 64: Ennahar, S., Y. Cai and Y. Fujita (2003) Phylogenetic Diversity of Lactic Acid Bacteria Associated with Paddy Rice Silage as Determined by 16S Ribosomal DNA Analysis. Appl. Environ. Microbiol. 69: Ezaki,., Y. Hashimoto and E. Yabuuchi (1989) Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacteria strains. International Journal of Systematic Bacteriology 39: (1997) PCR 16S rrna -- 12: McDonald P., N. Henderson and S. Heron (1991) he Biochemistry of Silage. 2nd ed. Chalcombe Publications. Berkshire. pp (1973). 44: (1999). 9: : (1986). 57:
12 Ohmomo, S., O. anaka, H. Kitamoto and Y. Cai (2002) Silage and microbial performance, old story but new problems. Japan Agricultural Research Quarterly 36: (1992)... pp (1971). 42: Saitou, N. and M. Nei (1987) he neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol.Evol. 4: Schleifer, K.H. and W. Ludwing (1989) Phylogenetic relationships among bacteria. In: he Hierarchy of life. Fernholm B, Bremer K, Jprnwall (Eds.), Elsevier Science Publishers BV, Amsterdam. pp (2000) 16S rrna. 57: (1996) ()... pp annock, G.W. (1999) Probiotics -A Critical Review. Horizon Scientific Press, Norfolk, pp.1-4. hompson, J.D., D.G. Higgins and.j. Gibson (1994) CLUSAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighing position-specific gap penalties and weight matrix choice. Nucleic Acid Re s. 22: (2000) HEALH DIGES 15: 1-8. Woese C. R.(1987) Bacterial Evolution. Microbiol. Rev. 51: (1986). R and D.. pp Zhang, J., Y. Cai, R. Kobayashi and S. Kumai (2000) Characteristics of lactic acid bacteria isolated from forage crops and their effects on silage fermentation. J. Sci. Food Agric. 80: January, National Institute of Agrobiological Sciences
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