Metagenomics-based unknown pathogeny rapid identification system and analysis method

A metagenome and genome technology, applied in the field of unknown pathogen analysis system based on metagenomics, can solve the problem that patients cannot determine the pathogen

Inactive Publication Date: 2013-07-03
SHANGHAI CENT FOR BIOINFORMATION TECH
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  • Abstract
  • Description
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Problems solved by technology

Even in the outbreak of common infectious diseases, there are still a considerable number of patients whose pathogens cannot be identified

Method used

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  • Metagenomics-based unknown pathogeny rapid identification system and analysis method
  • Metagenomics-based unknown pathogeny rapid identification system and analysis method
  • Metagenomics-based unknown pathogeny rapid identification system and analysis method

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Experimental program
Comparison scheme
Effect test

Embodiment 116

[0181] Correction of embodiment 1.16S rRNA copy number influence

[0182] 1. Datasets used

[0183] Here we used mouse 16S ribose from Zhang (Zhang, C. et al. Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice. Isme J 4, 232-241, doi: ismej2009112) et al. Body gene sequences, including 29343 16S ribosomal RNA gene sequences, these sequences were analyzed by Meta-All, and the species composition structure of a mouse intestinal bacterial community could be obtained.

[0184] 2. Restore the bacterial population structure

[0185] a.Traditional way

[0186] The primer pairs used are listed in the table below:

[0187]

[0188] Example of Oral Metagenomics Sample Analysis

[0189] Oral bacteria and oral diseases are closely related, and dental caries is the most common type of oral diseases in children. Scientific research shows that the development of dental caries is closely related to pathogenic bacteria...

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Abstract

The invention provides a metagenomics-based unknown pathogeny rapid identification system and an analysis method. Unknown pathogeny is identified and analyzed by applying a metagenomics-based method. The metagenomics-based unknown pathogeny rapid identification system comprises a sequencing quality control system, a Meta-All analysis system, an NeSSM second-generation sequencing simulation system, a pathogeny database system and a pathogeny composition comparing and analyzing unit, wherein the sequencing quality control system is used for carrying out quality analysis on sequencing data and removing part the sequencing quality of which does not accord with the requirement; the Meta-All analysis system is used as a main body of the metagenomics-based unknown pathogeny rapid identification system and is used for analyzing the species composition structure in a metagenomic library from the sequencing data; the NeSSM second-generation sequencing simulation system is used as an independent part to be capable of generating simulating sequencing data; the pathogeny database system automatically updates database resources needed to be used by the Meta-All analysis system; and the pathogeny composition comparing and analyzing unit is used for comparing composition structures of pathogenies in metagenomic libraries from different sources according to a species composition table and finding out a pathogeny with high correlation with diseases. The metagenomics-based unknown pathogeny rapid identification system has the advantages that the range of identifying the unknown pathogeny can be rapidly reduced by using the metagenomics-based method, and thus the identification speed is increased; and meanwhile a fully-unknown pathogeny can be analyzed from similar pathogenies.

Description

technical field [0001] The invention relates to the analysis of unknown pathogens, in particular to an unknown pathogen analysis system and analysis method based on metagenomics. Background technique [0002] Due to changes in various factors such as climate, ecology and human behavior, many infectious diseases caused by unknown pathogens have emerged, such as Nipah virus and SARS. Even in the outbreak of common infectious diseases, there are still a considerable number of patients who cannot identify the pathogen. Therefore, a platform for rapid detection of unknown pathogens is particularly important. It can help identify or narrow the scope of suspicious pathogenic microorganisms in the early stages of infectious disease outbreaks, so as to respond more quickly, deploy targeted prevention and control measures, and reduce disease prevalence. social and economic losses. [0003] Compared with the existing pathogen detection methods, the use of metagenomics to infer the co...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/22
Inventor 韦朝春蔡锴晔宣黎明贾鹏刘雷李亦学
Owner SHANGHAI CENT FOR BIOINFORMATION TECH
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