:B : (2011)

Transcript

1 MLSA ( ) : 16S rrnahsp60rpobatpdtuf (MLSA) :MLSA; ; :Q :B : (2011) Research progress of multilocus sequence analysis (MLSA) for rapid identification of Bifidobacterium species ZHAO TingCHENG Chi (China National Research Institute of Food & Fermentation Industries China Center of Industrial Culture Collection Beijing China) Abstract: This paper reviewed and evaluted the use of 16S rrnahsp60rpobatpdtuf gene part sequences as species identification tools for Bifidobacterium Strain sequences were derived from GenBank datebase Phylogenetic analysis showed that the multilocus sequence analysis(ml- SA) approach to Bifidobacterium taxonomy was possible and the discriminary of MLSA was higher than 16S rrna. Keyword: MLSA;Bifidobacterium;gene;Identification Pribram Tissieria 1938Prevot Bifidibacterium Bifidobacterium (Bifidobacterium) 1980SKERMAN [1] (Aprroved List of Bacterial Names) 7 [3] 36 9 (B.bifidum) [4] 16S rrna 30 16S : rrna 2004Liesbeth [5] DNA-DNA (Multilocus Sequence Analysis MLSA) (B. lactis) (B. animalis subsp. lactis);2002 Sakata [6] 16S [2] rrnahsp6016s -23S ITS DNA - hsp60rpobatpdgroeltuf 1 (Bifidobacterium)1899 Tissier 1924Orla-Jensen : : (No.2007BAK36B06) : (1980-) : 46 (AFLP) atpdgroel DNA (B.infantis) (B.suis) (B.longum) 3 (B.longum);2008Mattarelli [7] DNA- DNA 16S rrna hsp60 (RAPD) (DGGE) (PAGE) (B.longum) 3 : (B.longum subsp. longum) (B.longum subsp. in fantis) (B.longum

2 Monographs subsp. suis) 2010Jiri [8] B. actinocoloniiformeb. bohemicum Min-Soo [10] [9] B. stercoris Hidetoshi B. kashiwanohense 2 16S rrna Stackebrandt [11] 16S rrna 97% (1 )GenBank 16S rrna (Bacillus subtilis) NBRC T MEGA4.1 Kimura 1 16S rrna 1000 ( 1) : 16S rrna B.longum subsp. longum B.longum subsp. suis B.longum subsp. infantis B.breve Kimura %~99.7%; groel B.animalis subsp. animalisb.animalis subsp. lactisb.choerinumb.pseudolongum 1 ; PCR %~99.3%; B.adolescentisB. stercorisb.ruminantiumb.dentium hsp60 (2): B.longum 97.5%~99.4%;B.bifidum subsp. longumb.longum subsp. suisb.longum subsp. in- fantis 97.0% 98.4%98.8%98.4% 94.7%; B.animalis subsp. animalisb. 3 (ML- animalis subsp. lactis SA) 97.6% 85.7%; B.breve 94.7%; B.adolescentis (2~5 ) GenBank 92.6%;B.bifidum hsp60rpobatpdtuf hsp % (heat-shock protein)rpob RNA β (RNA polymerase β-subunit gene)atpd ATP F1 β (ATP synthase F1 beta subunit)groel (groel protein)tuf Tu(elongation factor Tu) Escherichia coli K-12 MEGA4.1 rpob (3): B.longum subsp. longumb.longum subsp. infantis 98.1% 95.6%; B.animalis subsp. 1 B.adolescentis B.bifidum B.breve B.longum subsp. infantis B.longum subsp. longum B.animalis subsp. animalis B.animalis subsp.lactis ATCC T ATCC T ATCC T ATCC T ATCC T BBMN68 ATCC T DSM T 16S rrna AP AB AB AB M58739 D86185 AB hsp60 AF AY AF AF AF AY AY GenBank rpob atpd AP AY EU AY EU AY CP AY EU CP EU AY CP AY groel AY AY tuf AY AY AY AY AY AY AY Vol.39No (total 247) 47

3 Monographs hsp60 rpob atpd groel tuf hspf1 hspr2 hspbf1 hspbr2 biff bifr bifr2 atp1 atp2 gro1 gro2 bif1 bif %; B.adolescentisB.pseudocatenulatum (B.longum)3 PCR 5 -CAGGCGAGGATCTTGGT-3 5' -ATCGCCAAGGAGATCGAGCT -3' (hspf1-hspr2) 644 bp 5' -AAGGTGCCGCGGATCTTGTT -3' (hspbf1-hspbr2) 680 bp 5' -CCGACCATCACCAACGATGG -3' 5' -CAGAACTTGAACGTGCCACG -3' 5' TCGATCGGGCACATACGG -3' (biff-bifr) 351bp 5' CGACCACTTCGGCAACCG -3' (biff-bifr2) 523 bp 5' ACAAGATCAACCGCAAGC -3' 5' -CACCCTCGAGGTCGAAC-3' 1133bp 5' -CTGCATCTTGTGCCACTTC-3' 5'-GACCATCACCAACGATG-3' 1158bp 5'-GCTCCGGCTTGTTGGC-3' 5 -GAGTACGACTTCAACCAG-3 825bp 97.5% 96.9%;B.bifidum 96.3% atpd (4): B.longum subsp. longumb.longum subsp. suisb.longum subsp. infantis 98.7% 97.1% 96.9% 95.6%; B.animalis subsp. animalis B.animalis subsp. lactis 97.2% 94.1%; B.breve 95.6%; B. adolescentis 92.8%;B.bifidum 94.1% tuf (5): B.longum subsp. longumb.longum subsp. infantisb.bifidum 96.4% 94.0% 93.0%; B.animalis subsp. animalisb.animalis subsp. lactisb.breveb.magumb.cuniculi 96.4% 93.7% 94.3%92.8%; B.adolescentisB.ruminantium hsp % 16S rrnahsp60rpobatpdtuf hsp60rpobatpdtuf 16S rrna 2 (B.longum) (B.longum subsp. infantis) (B. longum subsp. longum)2 RAPD DGGE (ribotyp- [7] ing) 2002Sakata 3 rpob [6] RAPD animalisb.animalis subsp. lactis (B.longum)3 97.5% 2002Requena [12] (B.longum)3 94.3%; B.breve DGGE 2006Sakata [13] 48 ribotyping (B.longum)3

4 Monographs 4 atpd Byoung [17] rpob rpob 84.1%~99.0% [18] hsp60 hsp60 Ventura [19] tuf 16S rrna ;Sheu [20] tuf PCR 16S rrna Zeigler [21] DNA Richter [22] ANI(Average Nucleotide Identity) DNA ANI 4 MLSA Naser [15] MLSA (Enterococcus) [14] Naser phesrpoa MLSA (B.adolescen- 16S rrna tis) (B.bifidum) (B. breve)3 Lactobacillus amylophilus LMG 11400NRRL B-4435 Lactobacillus amylotrophicus McTaggart [16] gyrb16s rrnaseca1hsp65rpob tuf 3 MLSA 3 (B.longum)3 / D- B. longum subsp. longum B.longum subsp. infantis (IDF) B.longum subsp. suis IDF (Bifidobacterium pseudolongum) (EFSA) (QPS) 74 MLSA API 20 A (B. infantis) (B. lactis) (L. lactis subsp. diacetylactis) MLSA Vol.39No (total 247) 49

5 Monographs : [1] Probiotics in Food [M].World Health OrganizationFood and Agriculture Organization of the United Nations Rome2006 [2] MIET MPETER DRENATA Cet al.advantages of Multilocus Sequence Analysis for Taxonomic Studies:A Case Study Using 10 Housekeeping Genes in the Genus Ensifer(Including Former Sinorhizobium) [J]. Int J Syst Evol Microbiol : [3] SKERMAN et al.approved Lists of Bacterial Names [J].Int J Syst Bacteriol198030(1):225. [4] [5] LIESBETH M MARCO V RALF Z et al. Polyphasic Taxonomic Analysis of Bifidobacterium Animalis and Bifidobacterium Lactis Reveals Relatedness at the Subspecies Level: Reclassification of Bifidobacterium Animalis as Bifidobacterium Animalis Subsp Animalis Subsp nov and Bifidobacterium Lactis as Bifidobacterium Animalis Subsp Lactis Subsp nov [J]. Int J Syst Evol Microbiol : 1137?1143. [6] SAKATA S KITAHARA M SAKAMOTO M et al. Unification of Bifidobacterium Infantis and Bifidobacterium Suis as Bifidobacterium Longum [J]. Int J Syst Evol Microbiol : [7] MATTARELLI P BONAPARTE C POT B et al. Proposal to Reclassify the Three Biotypes of Bifidobacterium Longum as Three Subspecies: Bifidobacterium Longum Subsp Longum Subsp nov Bifidobacterium Longum Subsp Infantis comb nov and Bifidobacterium Longum Subsp Suis comb nov[j]. Int J Syst Evol Microbiol : [8] JIRI K JAN K JAKUB M et al.bifidobacterium Actinocoloniiforme sp nov and Bifidobacterium Bohemicum sp nov [J]. Two New Bifidobacteria from the Bumblebee Digestive Tracts. Int J Syst Evol Microbiol (2010 in Press) [9] MIN-SOO KSEONG W R JIN-WOO B et al.bifidobacterium Stercoris sp nov Isolated from Human Faeces[J]. Int J Syst Evol Microbiol : [10] HIDETOSHI M AKIYO N HIROMI O et al.bifidobacterium Kashiwanohense sp nov Isolated from Healthy Infant Faeces [J]. Int J Syst Evol Microbiol (2010 in Press) [11] STACKEBRANDT EGOEBEL B.Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rrna Sequence Analysis in the Present Species Definition in Bacteriology[J]. Int J Syst Evol Microbiol : [12] REQUENA T BURTON J MATSUKI et al. Identification Detection and Enumeration of Human Bifidobacterium Species by PCR Targeting the Transaldolase Gene [J]. Appl Environ Microbiol : [13] SAKATA S RYU C S KITAHARA M et al. Characterization of the Genus Bifidobacterium by Automated Ribotyping and 16S rrna Gene Sequences[J]. Microbiol Immunol : 110. [14] SABRI M. N FABIANO L T BART Het al.application of Multilocus Sequence Analysis(MLSA) for Rapid Identification of Enterococcus Species Based on rpoa and phes Genes [J]. Microbiology : [15] SABRI M N MARC V CINDY Set al.reclassification of Lactobacillus Amylophilus LMG and NRRL B as Lactobacillus Amylotrophicus sp nov [J]. Int J Syst Evol Microbiol : [16] MCTAGGART L R RICHARDSON S E WITKOWSKA M et al.phylogency and Identification of Nocardia Species on the Basis of Multilocus Sequence Analysis [J].Journal of Clinical Microbiology (12): [17] BYOUNG J K HEE-YOUN K YEO-JUN Y et al.differentiation of Bifidobacterium Species Using Partial RNA Polymerase β -subunit (rpob) Gene Sequences [J]. Int J Syst Evol Microbiol : [18] JIAN W Y ZHU L DONG X Z.New Approach to Phylogenetic Analysis of the Genus Bifidobacterium Based on Partial hsp60 Gene Sequences[J]. Int J Syst Evol Microbiol : 1633?1638. [19] MARCO V CARLOS C VALERIE M et al.analysis Characterization and Loci of the tuf Genes in Lactobacillus and Bifidobacterium Species and Their Direct Application for Species Identification [J]. American Society for Microbiology200369(11): [20] SHEN S J HWANG W Z CHENG Y et al.use of tuf Gene-based Primers for the PCR Detection of Probiotic Bifidobacterium Species and Enumeration of Bifidobacteria in Fermented Milk by Cultural and Quantitative Real Time PCR Methods [J].Journal of Food Science (8): [21] DANIEL R Z.Gene Sequences Useful for Predicting Relatedness of Whole Genomes in Bacteria [J]. Int J Syst Evol Microbiol : [22] RICHTER MROSSELLO M R.Shifting the Genomic Gold Standard for the Prokaryotic Species Definition [J].PNAS (45):