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High-similarity microorganism identifying and classifying method

A classification method and microbial technology, applied in special data processing applications, instruments, electrical digital data processing, etc., can solve the problems of inability to accurately identify and classify highly similar microorganisms, and achieve high accuracy and good application prospects

Active Publication Date: 2018-01-12
广东美格基因科技有限公司
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Problems solved by technology

[0006] The purpose of the present invention is to overcome the problems that existing methods cannot accurately identify and classify highly similar microorganisms. The inventors of the present invention have found that for highly similar bacteria, the main driving factor for the differentiation of microbial strains is the acquisition and loss of new functional genes, rather than Single nucleotide mutations provide an accurate method for the identification and classification of highly similar microorganisms

Method used

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Embodiment 1

[0028] Identification and classification of embodiment 1 Enterobacteriaceae

[0029] 1) Strain collection

[0030] In this case, a total of 916 sequenced Enterobacter genomes were collected, including 14 strains of Enterobacter, 384 strains of Escherichia, 45 strains of Klebsiella, 314 strains of Salmonella, and 14 strains of Serratia. There were 42 strains of Shigella and 103 strains of Yersinia pestis.

[0031] 2) Strain identification and classification

[0032] When all genera were mixed together for identification and classification, most genera could be classified better. However, it is difficult to distinguish between Shigella and Escherichia, and it is also difficult to distinguish between Enterobacter and Klebsiella, but the trend is obvious. However, Y. pestis and Y. pseudotuberculosis in Yersinia pestis were clearly distinguished from other Yersinia pestis species. These phenomena are basically consistent with the conclusions observed in clinical practice. Furt...

Embodiment 2

[0033] Identification and classification of embodiment 2 streptococci

[0034] 1) Strain collection

[0035] A total of 283 streptococcus strains were collected in this case, including 83 strains of S.agalactiae, 7 strains of S.mitis, 8 strains of S.oralis, 38 strains of S.mutans, 119 strains of S.pneumoniae, 12 strains of S.pyogenes, and 10 strains of S. .suis, and 6 strains of S.thermophilus.

[0036] 2) Strain identification and classification

[0037] Cluster analysis of the 283 Streptococcus strains showed that all species could be well distinguished, including S.oralis and S.mitis. S.oralis and S.mitis are highly similar in microbial taxonomy, and were once considered to be the same species unit. Based on the non-similarity clustering of gene content, the two types of streptococci have obvious distinctions, which can be considered to belong to different microbial species.

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Abstract

The invention discloses a method for identifying and classifying highly similar microorganisms, which comprises: (1) using eggNOG database to compare the protein sequences encoded by the microbial genomes, assigning an eggNOG gene ID to each microbial genome, and generating an eggNOG database based on eggNOG database (2) Calculate the gene content dissimilarity between different microorganisms to be tested in the gene spectrum to obtain a dissimilarity matrix; (3) Perform cluster analysis on the matrix, and cluster microorganisms with similar gene content as A cluster, judged as the same type of microorganisms, completes the identification and classification of microorganisms. Aiming at highly similar microorganisms, the method of the present invention creatively proposes that the main driving factor for differences at the level of microorganisms is the gain and loss of genes, rather than the nucleic acid site mutation that is often considered by traditional methods. The invention has extremely high accuracy for the identification and classification of highly similar microorganisms, and has a good application prospect.

Description

technical field [0001] The invention belongs to the technical field of microorganism identification and classification, and more specifically relates to a method for identifying and classifying highly similar microorganisms by calculating the dissimilarity between the gene contents contained in the genomes of different microorganism strains. Background technique [0002] Identification and classification of microorganisms is a fundamental problem in microbiology research. The traditional method mainly observes the morphological characteristics of microorganisms through a microscope, and designs related experiments to measure the physiological and biochemical parameters of microorganisms, so as to judge the type of microorganisms. However, this type of method is complicated in experiments, lacks quantitative standards, and the parameters measured by different experimenters and different laboratories are not the same. Therefore, microbiology researchers are committed to findi...

Claims

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Application Information

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IPC IPC(8): G06F19/22G06F19/24
Inventor 屠奇超周集中束文圣叶脉李猛毛喆
Owner 广东美格基因科技有限公司
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