不同来源泡菜中乳酸菌的16S-23S rDNA间隔序列扩增及种群多样性分析

对不同来源的三种泡菜进行乳酸菌分离,并应用16S-23SrDNA间隔序列扩增指纹图谱结合16SrDNA测序对分离株进行种群多样性分析。结果显示在368株革兰氏阳性、接触酶阴性的产酸细菌中存在7个不同的分子指纹图谱(A～G型),其中杆菌指纹图谱为A、B和D型,球菌的指纹图谱为C、E、F和G型,不同来源的泡菜样品中乳酸菌谱型构成具有明显差异,其中52.3%(193/368)菌株扩增指纹图谱属于E型,显示了E型菌株是泡菜中的优势菌。从不同指纹图谱的菌株中随机挑取25株分离株进行16SrDNA扩增和测序分析,比对结果表明A型指纹图谱菌株属于Lactobacillus acidophilus;B和D型指纹图谱菌株属于Lactobacillus casei;E和G型指纹图谱菌株属于Lactococcus lactis;C和F型指纹图谱菌株属于Enterococcus sp.。在三种泡菜样品(a、b、c)中存在不同的乳酸菌种群构成,其中样品a和b菌群构成较为接近,而样品c中的菌群与a和b在构成上具有显著差异。本研究结果为泡菜发酵剂研究提供了基础数据及分析方法。     

Restriction fragment length polymorphism analysis of 16S rRNA genes in lactic acid bacteria isolated from red wine

Various lactic acid bacteria isolated from wine and alcoholic drinks attempted to identified by restriction fragment length polymorphism (RFLP). Oenococcus oeni strains exhibited unique RFLP patterns by HaeIII-digestion of 12 reference strains. We performed RFLP analysis using the AccII or HaeIII enzyme for 44 strains isolated from red wine and the results indicated profiles identical to O. oeni type strain. O. oeni does not exhibit interspecific diversity. Thus, the use of RFLP analysis of 16S rDNA is useful in the identification of O. oeni strains isolated from wines.     

利用16S rDNA序列及tuf-RFLP鉴定蒙古国发酵乳中的乳酸菌

运用16S rDNA序列分析和tuf-RFLP技术对采于蒙古国扎布汗省的25份发酵乳样中分离出的110株乳酸菌进行鉴定。首先将分离的110株乳酸菌的16S rRNA基因进行扩增,测序并构建系统发育树,初步鉴定为41株嗜热链球菌,40株瑞士乳杆菌,11株德氏乳杆菌保加利亚亚种,2株发酵乳杆菌,1株乳明串珠菌,2株肠膜明串肠膜亚种,1株乳酸乳球乳酸亚种和12株属于干酪族的菌株。由于干酪乳杆菌族的16S rDNA序列差异很小,故采用tuf-RFLP技术对这12株进行了进一步的验证,通过分离菌株与模式菌株tuf-RFLP图谱的比较分析,结果表明这12株菌均为干酪乳杆菌。     

Genus-specific profile of acetic acid bacteria by 16S rDNA PCR-DGGE

An effective method for grouping acetic acid bacteria (AAB) genera was defined and evaluated as a tool for preliminary screening of the major AAB species involved in vinegar production. Acetobacter, Gluconobacter, Gluconacetobacter, Asaia, Neoasaia, Saccharibacter, Frateuria and Kozakia AAB strains were screened on the basis of the 16S rDNA sequences using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) technique. The DGGE profile of all the strains tested, consisted of one single band of approximately 330 bp for each strain and allowed their clustering. The results obtained clearly reflected in silico phylogenetic analysis of the AAB species used in this study, in fact, the species with a higher 16S rDNA sequence homology showed a similar electrophoretic profile. In particular almost all the species belonging to the genus Gluconacetobacter showed a DGGE pattern nearly identical and well distinct from all the other AAB genera. Furthermore by PCR-DGGE it was possible to clearly group the species more frequently recovered from vinegar fermentation which are mainly distributed in the genera Acetobacter, Gluconobacter and Gluconacetobacter.     

Rapid discrimination of Salmonella isolates by single-strand conformation polymorphism analysis

A molecular typing technique was developed for the differentiation of Salmonella isolates based on single-strand conformation polymorphism (SSCP) analysis of amplicons generated by PCR. Amplicons from parts of the fimA (both the 5' and 3' ends), mdh, invA, and atpD genes were generated separately from a panel of Salmonella strains representing Salmonella bongori, and four subspecies and 17 serovars of Salmonella enterica. These amplicons were subjected to SSCP analysis for differentiation of the salmonellae on the basis of different conformational forms arising due to nucleotide sequence variations in the target genes. Several distinct SSCP banding patterns (a maximum of 14 each for atpD and fimA 3' end) were observed with this panel of Salmonella strains for amplicons generated from each target gene. The best discrimination of Salmonella subspecies and serovar was achieved from the SSCP analysis of a combination of at least three gene targets: atpD, invA, and either mdh or fimA 3' end. This demonstrates the applicability of SSCP analysis as an important additional method to classical typing approaches for the differentiation of foodborne Salmonella isolates. SSCP is simple to perform and should be readily transferable to food microbiology laboratories with basic PCR capability.     

16S rDNA在乳酸菌菌种鉴定及聚类分析上的应用

近年来,微生态制剂日益受到市场关注。市售微生态食品以益生菌酸奶或乳酸饮料为主,其中活的乳酸菌含量及菌株特性是决定微生态制剂质量的关键。目前常用的菌种鉴定技术包括生理生化方法或PCR方法,前者工作量大周期长,后者需要专业人员操作,且难以区分死活细菌。本文选取了11种市售的乳酸菌产品,采用MC、MRL、TPY等乳酸菌专用培养基进行乳酸菌计数及菌种分离,进一步用荧光定量PCR方法验证了产品中常规培养法难以分离的双歧杆菌,在此基础上,采用Riboprinter基因指纹图谱分析仪,对分离自11种酸奶样品的16株乳酸菌菌进行了核酸水平的鉴定,建立了16S rDNA聚类分析分子图谱,方便并简化对微生态产品的质量进行\     

烟草可培养内生细菌16S rDNA的PCR-RFLP和系统发育分析

为了解烟草内生细菌的多样性,采用改良的NA培养基和稀释平板法从不同生长期的烟草的根、茎、叶中分离得到127株内生细菌.利用细菌16S rDNA特异引物扩增得到16S rDNA的部分片段,长约700 bp,分别用内切酶MspⅠ、HaeⅢ、AfaⅠ、HinfⅠ对扩增产物进行限制性酶切.16S rDNA PCR-RFLP分析中,在100％相似性水平处,除了cj23、ty16、cg23、wy6、cj25、wy13、my23、ty7、cj14、cg25、cg2、cj13、my11,my27单独成群外,其余菌株分为15个分类操作单元,其中Otu1、Otu2,Otu27类群最大,分别包括了27、18,26个菌株.对29个代表菌株16S rDNA序列系统发育分析表明,这些菌株主要分布于芽孢杆菌(Bacillus)分支,其余菌株分布于葡萄球菌属(Staphylococcus)、微杆菌属(Microbacterium)、单胞菌属(Sphingomonas)、中华根瘤菌属(Sinorhizobium)、土壤杆菌属(Agrobacterium)、根瘤菌属(Rhizobium)、纳西杆菌属(Naxibacter)、贪铜菌属(Cupriavidus)、寡养食单胞菌属(Stenotrophomonas)、不动杆菌属(Acinetobacter)、假单胞菌属(Pseudomonas)、肠杆菌属(Enterobacter)、泛菌属(Pantoea)、克雷伯菌属(Klebsiella)、Bifissio属系统发育分支.通过Shannon多样性指数对不同生长期分离到的菌株进行多样性分析和比较,结果表明团棵期叶片中分离到的内生细菌多样性最大,随后是旺长期,苗期次之,成熟期最小.     

16S rDNA克隆法分析小曲优势细菌

用16S rDNA克隆法对某酒厂小曲中优势细菌进行分析,以期探讨强化酵母菌制曲后酒体风味变差的问题.用SDS-酶裂解法提取小曲总DNA,采用细菌通用引物对用PCR方法扩增其16S rDNA,并对PCR产物进行克隆与测序分析.结果表明,小曲中的优势细菌种类是以植物乳杆菌为主的乳酸菌.故强化制曲后发酵生产的白酒中乳酸乙酯含量增加,乙酸乙酯含量下降,造成酒整体风味变差.     

Parallel analysis of 7 food-borne pathogens using capillary electrophoresis-based single-strand conformation polymorphism

Capillary electrophoresis-based single-strand conformation polymorphism (CE-SSCP) coupled with multiplex polymerase chain reaction (PCR) method was used for the detection of 7 pathogens associated with foodborne illness, including Salmonella enterica, Clostridium perfringens, Bacillus cereus, Listeria monocytogenes, Yersinia enterocolitica, Vibrio parahaemolyticus, and Escherichia coli O157:H7. The method was applied to model food systems, both of culture medium and cooked rice. The detection limit of individual microbes was in the range of 10¹–10³ CFU/g, and that of the mixture of 7 microbes was 10³ CFU/g in the cooked rice sample. This method allowed the detection and identification of all 7 food-borne pathogens within 5 hr without the requirement for enrichment steps.     

16S rDNA序列关键位点的信息论分析

16S rDNA中含有较多的菌种特异性信息,但是如何使用这些信息进行菌种鉴定却因不同菌种间序列的特征变化缺少规律而变得困难。作者使用信息论方法对那些种内较保守,种间变异明显的关键位点进行研究。结果表明,16S rDNA序列中仅有少数位点对菌种的分类是重要的。基于少数关键位点的相似度比传统的全序列鉴定有着更好的统计学特性。     

16S rRNA gene-based analysis of microbial community by whole-genome amplification and minigel-single-strand conformation polymorphism technique

We have developed an analytical technique for the 16S rRNA gene that comprises whole-genome amplification and the polymerase chain reaction (PCR)-minigel-single-strand conformation polymorphism technique (WGA-SSCP). Under optimal conditions, SSCP bands could be detected when genomic DNA from bacteria of interest comprised 0.5% or more of the specimen. This method will be effective for the identification of nonculturable bacteria in a microbial community.     

熟制鲍鱼残留细菌的分离及16S rDNA鉴定

为控制熟制鲍鱼残留的细菌污染,采用平板划线分离技术对烘制加工后鲍鱼中残留的主要菌群进行分离,并通过菌落形态观察、革兰氏染色分析和16S rDNA 序列比对等方法对其进行鉴定. 结果表明,残留在烘制加工后鲍鱼的主要菌群有希瓦氏菌属、不动杆菌属、库特氏杆菌属、海洋类香菌、蜡样芽孢杆菌、肠杆菌属、彭氏变形杆菌等.     

创伤弧菌16S-23S rDNA间区变形梯度凝胶电泳多态性分析

目的 建立创伤弧菌基因分型的新方法,了解创伤弧菌的分子特征.方法 应用PCR-变形梯度凝胶电泳(PCR-DGGE)技术对创伤弧菌的16S-23S rDNA间区(16S-23S rDNA intergenic spacer regions,ISR)多态性进行分析比较,结合药敏试验,以进一步验证分离菌株之间的亲缘关系.结果 ISR-PCR将创伤弧菌菌株扩增出4条约900、750、650、550 bp大小不同的条带;同时,创伤弧菌的ISR-DGGE序列表现出明显的株间差异,18株共产生了16种不同的指纹图谱;聚类分析将所有的细菌分为两大类,相似性分别为0.65和0.71;亲缘关系较近的菌株具有不同于关系较远的菌株的耐药谱,与ISR-DGGE指纹图谱分析相一致.结论 这种分子操作技术完全能够用于创伤弧菌株型的调查与鉴定,为创伤弧菌的基因分型提供了一种新的方法.     

酸马奶中乳杆菌Lb.casei.Zhang和ZL12-1的16S rDNA基因序列及聚类分析

利用遗传学方法对分离自内蒙古锡林郭勒盟牧区采集的酸马奶样品中的乳杆菌Lb．casei．Zhang和ZL12-1的16S rDNA扩增与测序．并将结果与同属的乳杆菌作同源性分析，建立系统发育树，以求更准确地确定其归属，为益生菌的筛选奠定基础。结果表明，菌株Lb.casei.Zhang标准菌株Lb．casei ATCC334^T同源性为100％，菌株zLl2—1与标准Lb.gallinanum ATCC 33199^T的同源性为98％。结合系统发育树及16S rDNA的部分序列分析结果，将Lb.casei.Zhang判定为Lb．caseissubsp.casei.ZL12-1鉴定为Lb.gallinanum，这与传统分类方法所得鉴定结果一致。     

Rapid identification and classification of bacteria by 16S rDNA restriction fragment melting curve analyses (RFMCA)

The aim of this work was to evaluate restriction fragment melting curve analyses (RFMCA) as a novel approach for rapid classification of bacteria during food production. RFMCA was evaluated for bacteria isolated from sous vide food products, and raw materials used for sous vide production. We identified four major bacterial groups in the material analysed (cluster I-Streptococcus, cluster II-Carnobacterium/Bacillus, cluster III-Staphylococcus and cluster IV-Actinomycetales). The accuracy of RFMCA was evaluated by comparison with 16S rDNA sequencing. The strains satisfying the RFMCA quality filtering criteria (73%, n=57), with both 16S rDNA sequence information and RFMCA data (n=45) gave identical group assignments with the two methods. RFMCA enabled rapid and accurate classification of bacteria that is database compatible. Potential application of RFMCA in the food or pharmaceutical industry will include development of classification models for the bacteria expected in a given product, and then to build an RFMCA database as a part of the product quality control.     

Temperature gradient gel electrophoresis of the amplified product of a small 16S rRNA gene fragment for the identification of Listeria species isolated from food

The development of a rapid method for the identification of Listeria spp. is described. It is based on the polymerase chain reaction amplification of a small fragment from the 16S rRNA gene followed by temperature gradient gel electrophoresis. Forty-five strains of Listeria spp. (Listeria monocytogenes, Listeria innocua, Listeria ivanovii, Listeria seeligeri, and Listeria welshimeri) were used for the optimization of the protocol. No differences were observed between the results of the identification of the strains tested using traditional methods and those obtained by polymerase chain reaction-temperature gradient gel electrophoresis analysis.     

Evaluation of PCR-single-strand conformational polymorphism analysis for identification of gram-negative histamine-producing bacteria isolated from fish

In this study, the previously established PCR-single-strand conformation polymorphism (SSCP) system for detecting and identifying gram-negative histamine-producing bacteria was evaluated. This system can detect and identify histamine-producing bacteria directly from seafood by the use of sequence polymorphisms of the histidine decarboxylase gene (hdc). First, we isolated 81 histamine-producing strains of bacteria from fish samples and analyzed the hdc gene by the PCR-SSCP system. The 22 newly obtained SSCP banding patterns were added to our database, and the utility of our modified database was tested in a second experiment consisting of 18 strains of histamine-producing bacteria isolated from 25 fish samples. Approximately 80% of the histamine-producing strains corresponded to those in the new database. Use of the database for PCR-SSCP analysis, including the band patterns newly added in this study, for the hdc gene makes it possible to more accurately identify histamine producers.     

哈尔滨风干肠中优势蛋白质降解菌筛选及16S rDNA鉴定

以哈尔滨风干肠中41株球菌为对象,进行降解蛋白质酶活力的研究。采用定性和定量两种方法,筛选具有降解蛋白质酶活力的菌株,并对筛选出的菌株通过提取其DNA,进行PCR扩增,16S rDNA序列测定,进行系统的分类鉴定。结果表明:41株菌中只有10株菌具有降解蛋白质酶活性,其中CHMS34.1、CHMS34.3、CHMS34.9、CHMS34.15,4株具有较高的降解蛋白质酶活力,其酶活力分别为282、312、310、305U。4株解蛋白质菌的16S rDNA序列与GenBank中的已知序列相似性很高,确定了CHMS34.1、CHMS34.15为Staphylo-coccus pasteuri种菌株,CHMS34.3为Staphylococcus simiae种菌株,CHMS34.9为Staphylococcus xylosus种菌株。