Method for identifying individual intestinal flora types based on SNP

A technology of intestinal flora and intestinal bacteria, applied in the fields of genomics, instrumentation, proteomics, etc., to achieve the effect of high sensitivity, selectivity, and high detection throughput

Active Publication Date: 2020-02-21
EZHOU INST OF IND TECH HUAZHONG UNIV OF SCI & TECH +1
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Problems solved by technology

Individuals in populations tend to have different and highly variable gut flora, however, it is theorized that populations also share a conserved set of microbial populations and genes that may be necessary for normal gut function

Method used

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  • Method for identifying individual intestinal flora types based on SNP
  • Method for identifying individual intestinal flora types based on SNP
  • Method for identifying individual intestinal flora types based on SNP

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Embodiment 1

[0044] A method to identify the type of intestinal flora of an individual based on SNP, taking the identification of the type of intestinal flora of the Hadza as an example, reference Figure 1~7 , The specific identification steps are as follows:

[0045] 1) Data collection: The whole genome sequencing data of Hadza human gut microbes (accession SRA582120) is obtained from the NCBI SRA database, the number of samples is 40, the data type is Illumina HiSeq 4000 single-end sequencing data, and the read length is 151bp. Among them, there were 8 samples in the dry season in 2013, 19 samples in the rainy season in 2014, and 13 samples in the dry season in 2014. Then use the fastq-dump command of sra tools to convert the obtained sra binary file into fastq, and then use the ILLUMINACLIP parameter to remove the linker. The LEADING and TRAILING parameters remove bases with a base quality of less than 5 from the head and tail of the sequence, respectively.

[0046] 2) Obtain the species c...

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Abstract

The invention belongs to the technical field of intestinal microorganisms, and particularly relates to a method for identifying individual intestinal flora types based on SNP, which comprises the following steps: S1, obtaining sequencing data of individual intestinal flora on a longitudinal sequence, and analyzing all species to obtain a species abundance table; S2, screening main components of intestinal flora; S3, analyzing and mining SNP of intestinal flora; and S4, identifying the type of the individual intestinal flora, and guiding the health early warning of the intestinal flora. The method for identifying the individual intestinal flora type based on SNP is based on the idea of microbiomics and bioinformatics, analyzes and excavates SNP sites of species with seasonal sequence for research, has high sensitivity and selectivity, is high in detection flux, can identify the individual intestinal flora type and guide intestinal flora health early warning, and can be used for monitoring and evaluating human health conditions.

Description

Technical field [0001] The invention belongs to the technical field of intestinal microbes, and particularly relates to a method for identifying the type of intestinal flora of an individual based on SNP. Background technique [0002] The large and complex dynamic microbial community in the human intestine has a profound impact on the body's own metabolic phenotype, including archaea, bacteria, viruses, and fungi, and contains more than 1,000 microorganisms. Individuals in a population often have different and highly variable intestinal flora. However, existing theories believe that a group of conservative microbial populations and genes are also shared between the population, which may be necessary for the normal function of the intestine. . [0003] Human intestinal microbes are mainly composed of five types of bacteria and one type of archaea (Euryarchaeota). The five main types of bacteria are: Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Verrucomicrobia. Fi...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/20G16H50/30
CPCG16B20/20G16H50/30
Inventor 宁康秦季玥朱雪谭重阳
Owner EZHOU INST OF IND TECH HUAZHONG UNIV OF SCI & TECH
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