(15) MAFF Microorganism Genetic Resources Manual No.15 Lactic acid bacteria isolated from silage DNA G+C 1999 1991a 1994 Lactobacillus plantarum Lactobacillus casei McDonald et al. 1991 2001 Ohmomo et al. 2002 Lactobacillus Leuconostoc Lactococcus, Enterococcus Pediococcus Weissella 1996 1999 2001 Cai et al. 1999b 1999d Zhang et al. 2000 Ennahar 2003 2001 1971 1973 1982 1986 1991b 1995 2001 10 mm KN 180 260 mm g SQ-202 1
g 10 g 90 ml 10 10-8 GYP 1992 MRS 1986 30 2-3 1 3 1 gcfu/g 2001b Sample Salt solution MRS agar GYP-CaCO3 BCP agar Acetate agar 30 2-3days MRS 5 2-3 2-3 2
MRS 10 Dimethyl sulfoxide NA Bacto-Beef Extract 3 g + Bacto-Peptone 5 g/l-80 0.5 ml MRS 1992 1985 Lactobacillus, Streptococcus, Pediococcus, Leuconosotoc 4 1996 1986 Bergey s Munual of Systematic Bacteriology Vol.2 16S RNA 1996 DNA GC 16S rrna DNA Ezaki et al.1989 1997 2000) 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. 1997 DNA GemBank/EMBL/DDBJ CLUSAL Whompson et al. 1994 Saitou and Nei 1987 3
(type strain) DNA DNA Gold Standard of axonomy species 70 DNA 50 3 Species Subspecies DNA-DNA homology value Closely related independent species 4
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 516027 Leuconostoc pseudomesenteroides 1999/11 1 516028 Leuconostoc sp. 1999/11 13 516029 Leuconostoc sp. 1999/11 29 516030 Leuconostoc sp. 1999/11 65 516031 Leuconostoc sp. 1999/11 516032 Lactococcus lactis subsp. lactis 1999/11 3 516033 Lactococcus sp. 1999/11 4 516034 Lactococcus sp. 1999/11 15 516035 Lactococcus sp. 1999/11 30 516036 Lactococcus sp. 1999/11 52 516037 Lactococcus lactis subsp. lactis 1999/11 6 516038 Lactococcus sp. 1999/11 16 516039 Lactococcus sp. 1999/11 67 516040 Lactococcus sp. 1999/11 21 516041 Lactococcus sp. 1999/11 23 516042 Lactococcus sp. 1999/11 37 516043 Lactococcus sp. 1999/11 44 516044 Lactococcus sp. 1999/11 57 516045 Weissella confusa 1999/11 5 516046 Pediococcus acidilactici 1999/11 17 516047 Pediococcus sp. 1999/11 36 516048 Pediococcus sp. 1999/11 39 516049 Pediococcus sp. 1999/11 53 516050 Pediococcus sp. 1999/11 70 5
MAFF 516051 Pediococcus sp. 1999/11 83 516052 Pediococcus sp. 1999/11 85 516053 Lactobacillus brevis 1999/11 66 516054 Lactobacillus sp. 1999/11 77 516055 Lactobacillus sp. 1999/11 78 516056 Pediococcus pentosaceus 1999/11 95 516057 Enterococcus faecalis 1999/11 90 516058 Enterococcus sp. 1999/11 92a 516059 Enterococcus sp. 1999/11 92b 516060 Lactobacillus rhamnosus 1999/11 22 516061 Lactobacillus sp. 1999/11 40 516062 Lactobacillus sp. 1999/11 43 516063 Lactobacillus sp. 1999/11 69 516064 Lactobacillus sp. 1999/11 73 516065 Lactobacillus sp. 1999/11 81 516066 Lactobacillus sp. 1999/11 87 516067 Lactobacillus plantarum 1999/11 7 516068 Lactobacillus sp. 1999/11 8 516069 Lactobacillus sp. 1999/11 48 516070 Lactobacillus sp. 1999/11 64 516071 Lactobacillus sp. 1999/11 68 516072 Lactobacillus sp. 1999/11 80 516073 Lactobacillus sp. 1999/11 88 516074 Lactobacillus sp. 1999/11 91 516075 Lactobacillus sp. 1999/11 94 516076 Lactobacillus sp. 1999/11 101 516077 Lactococcus lactis subsp. lactis 2000/6 1 516078 Lactococcus lactis subsp. lactis 2000/6 2 516079 Lactococcus lactis subsp. lactis 2000/6 10 516080 Lactococcus lactis subsp. lactis 2000/6 12 516081 Pediococcus acidilactici 2000/6 11 516082 Pediococcus acidilactici 2000/6 24 516083 Pediococcus acidilactici 2000/6 25 516084 Lactobacillus plantarum 2000/6 13 516085 Lactobacillus plantarum 2000/6 15 516086 Lactobacillus plantarum 2000/6 17 516087 Lactobacillus plantarum 2000/6 22 516088 Lactobacillus plantarum 2000/6 26 516089 Lactobacillus plantarum 2000/6 28 516090 Enterococcus faecalis 2000/6 16 516091 Enterococcus faecalis 2000/6 30 516092 Enterococcus mundtii 2000/6 18 516093 Lactobacillus sakei 2000/6 19 516094 Pediococcus pentosaceus 2000/6 20 516095 Lactobacillus brevis 2000/6 21 516096 Lactobacillus brevis 2000/6 23 516097 Lactobacillus brevis 2000/6 29 516098 Pediococcus acidilactici 2000/6 27 516099 Leuconostoc citreum 2000/2 1 516 Leuconostoc lactis 2000/2 2 516101 Lactobacillus casei 2000/2 3 516102 Lactobacillus ferintoshensis 2000/9 4 516103 Lactobacillus ferintoshensis 2000/9 5 516104 Leuconostoc citreum 2000/9 1 516105 Lactococcus lactis subsp. lactis 2000/9 2 6
516106 Enterococcus gallinarum 2000/9 3 516107 Leuconostoc citreum 2000/9 4 516108 Lactobacillus plantarum 2000/9 5 516109 Leuconostoc citreum 2000/9 6 516110 Weissella paramensenteroides 2000/9 7 516111 Pediococcus acidilactici 2000/9 9 516112 Leuconostoc citreum 2000/9 10 516113 Lactobacillus casei 2001/9 CO70 516114 Lactobacillus casei 2001/9 CO71 516115 Lactobacillus casei 2001/9 CO73 516116 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 14 21 4 18 11 32 39 4 11 7 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
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 36.9-48.5DNA-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. 1998 Pediococcus acidilactici Lactobacillus plantarum ph MRS ph 3.6 ph Pediococcus acidilactici 50 48Cai et al. 1999c 2001a 2002 1999 2000 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 (%) 38.0 36.9 39.3 44.4 39.2 DNA-DN A(%) Characteristic 95.5 88.6 85.5 98.2 85.0 Leuconostoc pseudo - mensenteroides RO1 Lactobacillus plantarum RO7 Weissella confusa RO5 Lactobacillus brevis RO66 Lactobacillus brevis RO97 DNAG+C (%) 40.8 45.5 48.5 48.0 46.1 DNA-DN A(%) 90.5 81.6 93.8 87.7 85.9 8
87 82 85 78 56 37 66 37 51 95 83 98 87 52 63 97 75 59 99 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 44 10 94 99 18 31 E. solitarius 87 96 48 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 12173 ( D87677) JCM 5887 ( D87679) JCM 5889 ( D88528) LMG 12287 ( AJ271329) DSM 20285 ( AJ271383) DSM 20331 ( AJ318414) DSM 20336 ( AJ305321) his study ( AF515227) DSM 20284 ( AJ305320) his study ( AF515229) LMG 10748 ( AJ301836) LMG 11426 ( AJ301837) LMG 6399 ( AJ301834) LMG 11423 ( AJ301830) DSM 20633 ( AJ276354) NCIMB 12901 ( Y18296) LMG 10747 ( AJ301835) LMG 10744 ( AJ301825) LMG 13129 ( AJ301833) LMG 13518 ( AJ301832) LMG 10745 ( AJ301826) LMG 13521 ( AJ301829) ACC 700915 ( Y11621) LMG 19486 ( AF286831) LMG 19487 ( AF286832) LMG 7937 ( AJ301831) his study ( AF515223) LMG 13084 ( AJ301841) LMG 11427 ( AJ301839) LMG 11740 ( AJ301828) LMG 12902 ( AJ301827) DSM 5634 ( AJ301840) NCDO 1769 ( X60646) his study ( AF515228) NCDO 617 ( X54261) NCDO 1869 ( X54259) ACC 700018 ( X53905) JCM 8735 ( AB012306) ACC 19257 ( M58836) ACC 19435 ( M58837) his study ( AF515224) his study ( AF515225) JCM 6125 (M35820) DSM 20189 ( S63851) LMG 18811 ( AF231131) NRIC 1722 ( AB022925) JCM 6123 ( AB023968) NRIC 1776 ( AB022923) DSM 8581 ( AF175403) NRIC 1539 ( AB023246) DSM 20343 ( M23035) DSM 20346 ( M23034) NRIC 1778 ( AB022921) NRIC 1777 ( AB023237) 5 Leuconostoc Lactococcus Pediococcus Enterococcus S RNAKnucNJ 0.02 K nuc 9
59 33 43 22 64 40 38 62 82 4 11 80 18 33 93 68 91 98 69 87 46 90 92 L. collinoides L. arizonensis 94 L. paraplantarum 61 L. plantarum L. pentosus 93 RO7 L. hilgardii L. kefiri 99 L. parabuchneri 65 93 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 27612 ( AB005893) JCM 11125 ( AF093757) DSM 10667 ( AJ306297) JCM 1149 ( D79210) JCM 1558 ( D79211) his study ( AF515222) DSM 20176 ( M58821) NRIC 1693 (AB024300) LMG 11457 ( AY026751) LMG 15133 ( AY026750) DSM 20057 ( M58811) ACC 14869 ( M58810) his study ( AF515220) his study ( AF515219) ACC 700308 ( Y11374) ACC 27651 ( M58830) DSM 20690 ( X95421) DSM 20203 ( X76330) ACC 29644 ( M58817) DSM 13238 ( AJ417500) JCM 10707 ( AF183558) DSM 20249 ( M58804) DSM 20017 ( M58829) DSM 20010 ( AJ270951) DSM 20505 ( M58831) LMG 18010 ( AF000162) ACC 7469 ( M58815) ACC 15820 ( D86516) ACC 334 ( D86517) DSM 20001 ( M58813) DSM 20003 ( M58809) LMG 17710 ( AF049745) DSM 12744 ( Y19167) JCM 10491 (AB033209) ACC 700692 ( Y17500) DSM 20444 ( M58824) DSM 20403 ( M58828) DSM 20452 ( M58826) DSM 20602 ( M58807) JCM 10991 ( AB048833) DSM 20509 ( M58803) ACC 11741 ( AF089108) DSM 20554 ( M59054) DSM 20655 ( M58808) JCM 5667 (AB001837) CCUG 42961 ( AJ251560) JCM 10692 (AB023836) 0.01 K nuc DSM 13345 ( AF126738) 74 99 94 91 86 47 90 74 83 76 49 94 61 44 L. reuteri L. vaginalis 93 L. panis L. oris L. pontis L. frumenti L. coleohominis L. amylophilus 68 58 70 71 L. johnsonii L. gasseri L. psittaci L. jensenii L. fornicalis 61 58 94 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 20016 ( L23507) NCC 12197 ( X61136) DSM 6035 ( X94230) DSM 4864 ( X94229) ACC 51518 ( X76329) DSM 13145 ( AJ250074) CCUG 44007 ( AJ292530) DSM 20533 ( M58806) CCUG 28746 ( Y16329) ACC 33200 ( AJ002515) DSM 20243 ( M58820) CCUG 42378 ( AJ272391) ACC 25258 ( AF243176) ACC 700934 ( Y18654) ACC 12315 ( M58823) ACC 9649 ( M58814) JCM 2 ( AB007908) DSM 6629 ( AJ306299) DSM 5661 ( AJ306298) DSM 11664 ( Y17361) DSM 20584 ( Y17362) DSM 20531 ( M58805) NCDO 2712 ( X61141) ACC 33199 ( AJ242968) ACC 4356 ( M58802) DSM 20749 ( M58801) NCDO 2345 ( X61140) DSM 20410 ( M23040) DSM 20190 ( M23037) DSM 14420 ( AY028260) DSM 20593 ( M23038) JCM 10695 ( AB023838) NCFB 803 (AB023238) NCFB 2973 ( X95981) JCM 1093 ( M23036) LMG 17699 ( AJ295989) DSM 14295 ( AF312874) his study ( AF515221) NCDO 1769 ( X60646) 6 Lactobacillus WeissellaS RNA KnucNJ 10
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