基于分子标识的工业微生物资源快捷分类与鉴定
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摘要
微生物是一类重要的生物资源，是现代工业生物技术发展的生物学基础。人类利用微生物资源已经产生了巨大的经济和社会效益。微生物资源被有效应用的基础是微生物的分离培养和分类鉴定。随着分子生物学理论和方法的不断发展，目前，微生物的分类鉴定已经在形态、生理生化等传统鉴定实验技术的基础上，更多的利用分子生物学的发展成果，通过分子标识的核苷酸序列及其解析实现微生物分离培养物的高效、快捷和准确鉴定。微生物核糖体DNA（rDNA）序列是微生物分类鉴定中最重要的分子标识。为确定rDNA序列在大规模工业微生物资源分类与鉴定中的应用可行性和应用价值，本文创建了微生物基因组DNA及其rDNA分子标识的快速高通量制备方法，研究了细菌16SrDNA序列、酵母和丝状真菌内部转录间隔区（Internal transcribed spacer, ITS）序列等分子标识在工业微生物资源分类与鉴定中的价值与意义。获得的主要研究结果如下：
（1）建立了核糖体DNA分子标识的快速制备方法，为工业微生物资源的批量、快捷分类与鉴定奠定了基础。研究了从基因组DNA释放到标识分子PCR扩增的各阶段影响因素，优化了不同种属微生物基因组DNA的通用制备方法，建立了一种快捷的工业微生物资源的批量鉴定方法，此方法中的基因组DNA制备过程耗时仅20min，并省去了有机溶剂抽提和蛋白酶、RNase等的处理步骤，可实现微生物资源的批量（96n个分离物）鉴定。此方法可应用于细菌、放线菌、酵母和丝状真菌等不同种属微生物资源的快捷分类鉴定。利用该方法对5296株不同种属的工业微生物资源保藏物进行了成功鉴定。
（2）研究了16S rDNA分子标识在细菌分类与鉴定中的价值，所研究的全部细菌分离物均可通过16S rDNA分子标识鉴定到属，绝大多数（82.5%）细菌分离物可直接鉴定到种。运用上述工业微生物资源批量、快捷分类鉴定方法，对3726株细菌分离物的16S rDNA进行了有效扩增、核苷酸序列测定、序列比对和分类鉴定，其中3073株细菌分离物可被成功鉴定到种一级，分属于210个种，45个属，占整个细菌分离物的82.5%；其余653株细菌分离物仅可鉴定到属，占整个细菌分离物的17.5%。研究中也发现，16S rDNA分子标识在芽孢杆菌属（Bacillus）和土芽孢杆菌属（Geobacillus）等少数菌属中的部分种间鉴定的敏感性不高。
（3）研究了ITS分子标识在丝状真菌分子鉴定中的普适性，所研究丝状真菌分离物中的99.4%可通过ITS分子标识鉴定到属，其中82.2%的分离物可直接鉴定到种。利用ITS序列同源性分析对832株丝状真菌分离物进行了分子鉴定，其中684株（82.2%）分离物可被成功鉴定到种，分属于84个种，33个属；143株分离物仅可鉴定至属一级水平，占整个丝状真菌分离物的17.2%。研究中也发现，ITS分子标识在曲霉属（Aspergillus）和青霉属（Penicillium）等少数菌属内部分种间鉴定的敏感性不高。本研究中，另有5株（0.6%）丝状真菌分离物尚不能通过ITS分子标识获得有效鉴定。
（4）研究了ITS分子标识在酵母分类鉴定中的适用性，所研究酵母分离物中的99.7%可通过ITS分子标识鉴定到属，其中94.3%的分离物可直接鉴定到种。利用ITS分子标识对738株酵母分离物进行了分类鉴定，有696株（94.3%）酵母分离物可被成功鉴定到种，分属于42个种，18个属；40株分离物仅能鉴定到属，占整个酵母分离物的5.4%。另有2株（0.3%）分离物尚不能通过ITS分子标识获得有效鉴定。
综上所述，本研究在建立批量、快捷和高效的微生物鉴定方法的基础上，研究确认了16S rDNA序列在细菌分类鉴定、ITS序列在酵母和丝状真菌分类鉴定中拥有很高的敏感性和特异性，可以将绝大部分的微生物分离物直接鉴定到种属。因此，细菌16SrDNA序列及酵母和丝状真菌ITS序列可以作为第一轮分类鉴定标识，用于微生物分离物的分类鉴定。微生物的鉴定可以也应该从rDNA开始。
Microorganism is one of the most important biological resources on the earth, also thebiological basis for the industrial biotechnology. Microbial resources applied in biotechnologyhave been contributing greatly to economic and social benefits. Identification of microbialresources is the key point to the development of biotechnology. Conventional microbialidentification has been based on the phenotype and biochemical characteristics. With theadvances in polymerase chain reaction (PCR) and DNA sequencing technologies, moleculartechniques have progressively been developed as standard approaches in studies dealing withmicrobial classification. The microbial taxonomy has shift from phenotypic to DNA-basedmolecular technology. In recent years, several molecular identification methods have beenestablished by making use of the variable domains of the rDNA sequences. With the aim toevalueate the feasibility and value of rDNA sequences applied in industrial microbialidentification, this study focused on the establishment of rapid method for microbial genomicDNA extraction and the applicability of molecular markers (bacterial16S rDNA, internaltranscribed spacer of yeasts and filamentous fungi) used in microbial taxonomy. The mainresults are as follows:
(1) A rapid, efficient approach for molecular markers prepartion in bulk wasestablished based on a novel rapid microbial genomic DNA extraction method. In thisstudy, a novel rapid and efficient DNA extraction method based on alkaline lysis which candeal with a large number of microbial isolates (96n) in the same batch was established. Thegenomic DNA required only20minutes to prepare, and eliminated the need for complexDNA purification protocols such as solvent extraction. The extracted genomic DNA can bedirectly used as template for molecular markers amplification using PCR assay. The amplifiedrDNA sequences were easy to identify by analysis. The extracted DNA also can be used toamplify other protein-coding genes for molecular identification. This method can be used forrapid systematic microbial identification. Up to now, we have already successfully identified5296strains (including bacteria, actinomycetes, filamentous fungi and yeast) based on thismethod.
(2) Evaluated the feasibility of16S rDNA sequence for systemic classification andidentification of bacterial isolates,82.5%of test strains can be assigned to species leveldirectly. The16S rDNA sequences of3726bacterial strains deposited in CICIM-CU (Cultureand information center of industrial microorganism of China universities) were amplifiedusing PCR reaction. The sequences were compared to reference data available at the GenBankdatabase by using BLAST (Basic local alignment search tool). The results shown all of teststrains were identified to genus level successful by16S rDNA sequence-based anaylsis. Mostof isolates (82.5%) were identified to species level which assigned to210species belongingto45genera. Some closely-related Bacillus and Geobacillus species have highly similar16SrDNA sequences, making16S rDNA sequence analysis-based identification problematic.
(3) Assessment of the sensitivity of ITS sequence for classification of filamentousfungal isolates,82.2%of test strains were assigned to species level successfully. The ITS regions of832fungal isolates were amplified by PCR and sequenced. The results of ITSsequences analysis shown most of fungal isolates (82.2%) were identified to species levelsuccessfully which assigned to84species belonging to33genera.143fungal isolates (17.2%)were identified to genus level merely which difficult to distinguished from each other becausepoor interspecies homology of ITS sequence, especially in genus Aspergillus and Penicillium.Only5strains (0.6%) cannot be identified based on ITS sequences analysis. Although ITSsequence may not be sufficiently sensitive for identifying some closely related taxa to specieslevel, it can be used as first-round molecular marker to systemic identification of bulk fungalisolates efficiently.
(4) Assessment of the sensitivity of ITS sequence for classification of yeast isolates,94.3%of isolates were assigned to species level by ITS sequence variability. The738yeast isolates deposited in CICIM-CU were identified by ITS regions sequence-basedalignment, the result shown696test strains (94.3%) were identified to species levelsuccessfully which assigned to42species belonging to18genera.40strains (5.4%) wereassigned to genus level merely.2strains (0.3%) cannot be identified based on ITS sequencesanalysis.The results shown the ITS sequence exhibits enough differences between yeasts, andcan be used in the discrimination of intra-and inter-species relationships.
In summary, based on the novel efficient method of microbial identification, this researchconfirmed the sequences of16S rDNA and ITS have sufficiently sensitive for identifyingbacterial, yeast and fungal isolates, respectively. Most of microbial isolates in this study canbe assiganed to species or genus level successfully by using these two molecular markers. Thepresent results clearly demonstrate that the16S rDNA and ITS region are sufficient asfirst-round molecualer markers used in microbial isolates identification. Therefore, microbialidentification can and should starts from the rDNA sequences.
（1）建立了核糖体DNA分子标识的快速制备方法，为工业微生物资源的批量、快捷分类与鉴定奠定了基础。研究了从基因组DNA释放到标识分子PCR扩增的各阶段影响因素，优化了不同种属微生物基因组DNA的通用制备方法，建立了一种快捷的工业微生物资源的批量鉴定方法，此方法中的基因组DNA制备过程耗时仅20min，并省去了有机溶剂抽提和蛋白酶、RNase等的处理步骤，可实现微生物资源的批量（96n个分离物）鉴定。此方法可应用于细菌、放线菌、酵母和丝状真菌等不同种属微生物资源的快捷分类鉴定。利用该方法对5296株不同种属的工业微生物资源保藏物进行了成功鉴定。
（2）研究了16S rDNA分子标识在细菌分类与鉴定中的价值，所研究的全部细菌分离物均可通过16S rDNA分子标识鉴定到属，绝大多数（82.5%）细菌分离物可直接鉴定到种。运用上述工业微生物资源批量、快捷分类鉴定方法，对3726株细菌分离物的16S rDNA进行了有效扩增、核苷酸序列测定、序列比对和分类鉴定，其中3073株细菌分离物可被成功鉴定到种一级，分属于210个种，45个属，占整个细菌分离物的82.5%；其余653株细菌分离物仅可鉴定到属，占整个细菌分离物的17.5%。研究中也发现，16S rDNA分子标识在芽孢杆菌属（Bacillus）和土芽孢杆菌属（Geobacillus）等少数菌属中的部分种间鉴定的敏感性不高。
（3）研究了ITS分子标识在丝状真菌分子鉴定中的普适性，所研究丝状真菌分离物中的99.4%可通过ITS分子标识鉴定到属，其中82.2%的分离物可直接鉴定到种。利用ITS序列同源性分析对832株丝状真菌分离物进行了分子鉴定，其中684株（82.2%）分离物可被成功鉴定到种，分属于84个种，33个属；143株分离物仅可鉴定至属一级水平，占整个丝状真菌分离物的17.2%。研究中也发现，ITS分子标识在曲霉属（Aspergillus）和青霉属（Penicillium）等少数菌属内部分种间鉴定的敏感性不高。本研究中，另有5株（0.6%）丝状真菌分离物尚不能通过ITS分子标识获得有效鉴定。
（4）研究了ITS分子标识在酵母分类鉴定中的适用性，所研究酵母分离物中的99.7%可通过ITS分子标识鉴定到属，其中94.3%的分离物可直接鉴定到种。利用ITS分子标识对738株酵母分离物进行了分类鉴定，有696株（94.3%）酵母分离物可被成功鉴定到种，分属于42个种，18个属；40株分离物仅能鉴定到属，占整个酵母分离物的5.4%。另有2株（0.3%）分离物尚不能通过ITS分子标识获得有效鉴定。
综上所述，本研究在建立批量、快捷和高效的微生物鉴定方法的基础上，研究确认了16S rDNA序列在细菌分类鉴定、ITS序列在酵母和丝状真菌分类鉴定中拥有很高的敏感性和特异性，可以将绝大部分的微生物分离物直接鉴定到种属。因此，细菌16SrDNA序列及酵母和丝状真菌ITS序列可以作为第一轮分类鉴定标识，用于微生物分离物的分类鉴定。微生物的鉴定可以也应该从rDNA开始。
Microorganism is one of the most important biological resources on the earth, also thebiological basis for the industrial biotechnology. Microbial resources applied in biotechnologyhave been contributing greatly to economic and social benefits. Identification of microbialresources is the key point to the development of biotechnology. Conventional microbialidentification has been based on the phenotype and biochemical characteristics. With theadvances in polymerase chain reaction (PCR) and DNA sequencing technologies, moleculartechniques have progressively been developed as standard approaches in studies dealing withmicrobial classification. The microbial taxonomy has shift from phenotypic to DNA-basedmolecular technology. In recent years, several molecular identification methods have beenestablished by making use of the variable domains of the rDNA sequences. With the aim toevalueate the feasibility and value of rDNA sequences applied in industrial microbialidentification, this study focused on the establishment of rapid method for microbial genomicDNA extraction and the applicability of molecular markers (bacterial16S rDNA, internaltranscribed spacer of yeasts and filamentous fungi) used in microbial taxonomy. The mainresults are as follows:
(1) A rapid, efficient approach for molecular markers prepartion in bulk wasestablished based on a novel rapid microbial genomic DNA extraction method. In thisstudy, a novel rapid and efficient DNA extraction method based on alkaline lysis which candeal with a large number of microbial isolates (96n) in the same batch was established. Thegenomic DNA required only20minutes to prepare, and eliminated the need for complexDNA purification protocols such as solvent extraction. The extracted genomic DNA can bedirectly used as template for molecular markers amplification using PCR assay. The amplifiedrDNA sequences were easy to identify by analysis. The extracted DNA also can be used toamplify other protein-coding genes for molecular identification. This method can be used forrapid systematic microbial identification. Up to now, we have already successfully identified5296strains (including bacteria, actinomycetes, filamentous fungi and yeast) based on thismethod.
(2) Evaluated the feasibility of16S rDNA sequence for systemic classification andidentification of bacterial isolates,82.5%of test strains can be assigned to species leveldirectly. The16S rDNA sequences of3726bacterial strains deposited in CICIM-CU (Cultureand information center of industrial microorganism of China universities) were amplifiedusing PCR reaction. The sequences were compared to reference data available at the GenBankdatabase by using BLAST (Basic local alignment search tool). The results shown all of teststrains were identified to genus level successful by16S rDNA sequence-based anaylsis. Mostof isolates (82.5%) were identified to species level which assigned to210species belongingto45genera. Some closely-related Bacillus and Geobacillus species have highly similar16SrDNA sequences, making16S rDNA sequence analysis-based identification problematic.
(3) Assessment of the sensitivity of ITS sequence for classification of filamentousfungal isolates,82.2%of test strains were assigned to species level successfully. The ITS regions of832fungal isolates were amplified by PCR and sequenced. The results of ITSsequences analysis shown most of fungal isolates (82.2%) were identified to species levelsuccessfully which assigned to84species belonging to33genera.143fungal isolates (17.2%)were identified to genus level merely which difficult to distinguished from each other becausepoor interspecies homology of ITS sequence, especially in genus Aspergillus and Penicillium.Only5strains (0.6%) cannot be identified based on ITS sequences analysis. Although ITSsequence may not be sufficiently sensitive for identifying some closely related taxa to specieslevel, it can be used as first-round molecular marker to systemic identification of bulk fungalisolates efficiently.
(4) Assessment of the sensitivity of ITS sequence for classification of yeast isolates,94.3%of isolates were assigned to species level by ITS sequence variability. The738yeast isolates deposited in CICIM-CU were identified by ITS regions sequence-basedalignment, the result shown696test strains (94.3%) were identified to species levelsuccessfully which assigned to42species belonging to18genera.40strains (5.4%) wereassigned to genus level merely.2strains (0.3%) cannot be identified based on ITS sequencesanalysis.The results shown the ITS sequence exhibits enough differences between yeasts, andcan be used in the discrimination of intra-and inter-species relationships.
In summary, based on the novel efficient method of microbial identification, this researchconfirmed the sequences of16S rDNA and ITS have sufficiently sensitive for identifyingbacterial, yeast and fungal isolates, respectively. Most of microbial isolates in this study canbe assiganed to species or genus level successfully by using these two molecular markers. Thepresent results clearly demonstrate that the16S rDNA and ITS region are sufficient asfirst-round molecualer markers used in microbial isolates identification. Therefore, microbialidentification can and should starts from the rDNA sequences.
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