Optimization method for accurate species identification of human flora through high-throughput 16S rDNA sequencing

An optimization method and high-throughput technology, applied in the fields of medicine and molecular biology, can solve problems such as lack of relative abundance information and inability to form sequences

Pending Publication Date: 2020-10-23
HANGZHOU GUHE INFORMATION TECH CO LTD
View PDF0 Cites 4 Cited by
  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Due to the lack of metagenomic sequencing data, there are only a small number of bacterial genome reference sequences, and the relative abundance information obtained from large-scale metagenomic sample sequencing is lacking. The correlation information of sequence composition abundance cannot be used in the identification of 16S rDNA sequence species in the past.

Method used

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View more

Image

Smart Image Click on the blue labels to locate them in the text.
Viewing Examples
Smart Image
  • Optimization method for accurate species identification of human flora through high-throughput 16S rDNA sequencing
  • Optimization method for accurate species identification of human flora through high-throughput 16S rDNA sequencing
  • Optimization method for accurate species identification of human flora through high-throughput 16S rDNA sequencing

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0076] Example 1. An optimized method for the accurate identification of human flora 16S rDNA high-throughput sequencing species, such as figure 1 described, including the following steps:

[0077] step 1),

[0078] 1.1) According to the WGS method, the samples from the same human tissue source are sequenced, so as to establish a human metagenomic sequencing database based on human microbial samples, so the human metagenomic sequencing data meet the following conditions: the species is human, and the sequencing method is WGS ( Whole genome sequencing), with a clear source of samples.

[0079] Sources of human metagenomic sequencing data that meet the above requirements include but are not limited to:

[0080] NCBI's sra database https: / / www.ncbi.nlm.nih.gov / sra;

[0081] https: / / www.ebi.ac.uk / metagenomics / ;

[0082] Explanation: The above two databases are existing metagenomic open data storage databases, which can be directly downloaded from the above to obtain the public...

Embodiment 2

[0107] Embodiment 2, this is the use of species identification and abundance calculation of high-throughput sequencing 16S rDNA sequences based on the database and model of the above-mentioned embodiment 1; specific operations include the following steps:

[0108] 1) Obtain sample high-throughput sequencing 16S rDNA sequence: Obtain the full-length or partial segment sequencing sequence of 16S rDNA through second-generation or third-generation high-throughput sequencing, and then follow the quality inspection and splicing of the above steps to obtain human 16S rDNA sequencing data .

[0109] The sample has a clear source of the human tissue part of the sample.

[0110] 2), first perform sequence alignment according to the type of sample source and the corresponding 16S species sequence database (16srDNA sequence database) in step 2) of Example 1 (common 16S comparison and analysis software such as DADA2 or Vsearch can be used), so as to obtain 16S sequence abundance degree; a...

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to view more

PUM

No PUM Login to view more

Abstract

The invention discloses an optimization method for accurate species identification of human flora through high-throughput 16S rDNA sequencing. The optimization method comprises the following steps: 1)establishing a human metagenome bacterium genome database based on human microorganism samples; 2) extracting full-length 16S rDNA sequences of the human metagenomic bacterium genome database, and establishing 16S rDNA species annotation databases of different human body parts; and 3) establishing a sample-strain 16S sequence abundance correlation network, and training a machine learning model byusing the data. The invention also provides a method for performing species identification and abundance calculation on the high-throughput sequencing 16S rDNA sequences by using the constructed database and model. According to the invention, the species classification resolution and accuracy of 16S rDNA can be greatly improved, so an analyst can find more accurate and clear strains according toresults.

Description

technical field [0001] The invention belongs to the fields of molecular biology and medicine; in particular, it relates to an optimized method for accurate identification of human flora 16S rDNA high-throughput sequencing species. Background technique [0002] With the maturity of sequencing technology and the decline of cost, researches related to human microbiome have discovered and accumulated more and more microbiome sequencing data, and obtained a large number of microbiome composition and its correlation with human health, disease and living conditions. data. Among them, 16S rDNA sequencing is a common sequence for bacteria and archaea. Its sequencing cost is low, its versatility is good, and it has low requirements for samples. Therefore, it has become the main research technology in the study of flora. 16S rRNA is the main ribosomal RNA in bacteria, corresponding to a gene sequence on the genomic DNA to become 16S rDNA. 16S rDNA identification refers to the identif...

Claims

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to view more

Application Information

Patent Timeline
no application Login to view more
IPC IPC(8): G16B30/10G16B30/20G16B40/00G16B50/30
CPCG16B30/10G16B30/20G16B40/00G16B50/30Y02A90/10
Inventor 金谷雷牛耀芳
Owner HANGZHOU GUHE INFORMATION TECH CO LTD
Who we serve
  • R&D Engineer
  • R&D Manager
  • IP Professional
Why Eureka
  • Industry Leading Data Capabilities
  • Powerful AI technology
  • Patent DNA Extraction
Social media
Try Eureka
PatSnap group products

Browse by: Latest US Patents, China's latest patents, Technical Efficacy Thesaurus, Application Domain, Technology Topic.

© 2024 PatSnap. All rights reserved.Legal|Privacy policy|Modern Slavery Act Transparency Statement|Sitemap