Metagenome 16S hypervariable region V3 based classification method and device thereof

Abstract

The invention discloses a metagenome 16S hypervariable region V3 based classification method and a device thereof. The method contains the following steps of: extracting DNA in microbial samples; carrying out amplification of metagenome 16S rDNA hypervariable region V3, carrying out Solexa database construction on amplification products, and simultaneously marking each sample by adding a connector with a label sequence in the process of database construction; mixing different samples with label sequences, sequencing by the use of a Solexa sequencing tool after mixing to obtain original sequencing sequences reads distinguished by labels; assembling by the use of reads overlapping relations to obtain hypervariable region V3 full-length sequences unique reads; and carrying out classification analysis on unique reads to accomplish classification of microbial population. By the adoption of the method and the device provided by the invention, classification of microbial population is accurate and sequencing cost is greatly reduced.

Description

technical field [0001] The invention relates to the technical field of bioinformatics analysis, in particular to a classification method and device based on the metagenomic 16S hypervariable region V3. Background technique [0002] In order to study the types of microbial populations in the biological environment, the general traditional methods include: direct cultivation of microorganisms, denaturing gradient gel electrophoresis (DGGE, Denaturing Gradient Gel Electrophoresis), terminal restriction endonuclease fragment length polymorphism (T- RFLP, Terminal Restriction Fragment Length Polymorphism), fluorescence in situ hybridization (FISH, Fluorescence In Situ Hybridization), PCR (polymerase chain reaction, Polymerase Chain Reaction) on possible microbial species; but these methods can only reveal the A very small number of microbial species. If metagenome analysis can be carried out, a relatively comprehensive catalog of microbial species can be obtained by directly con...

AI Technical Summary

Problems solved by technology

A major challenge for these revolutionary technologies is that the read lengths are too short to sequence the 16S rDNA of each individual, and thus its sequencing information is not sufficient to allow us to accurately classify microorganisms

In order to solve the problem of read length, some studies (Bacterial flora-typing with targeted, chip-based Pyrosequencing, BMC Microbiology 2007, 7: 108 doi: 10.1186 / 1471-2180-7-108, published on November 30, 2007) passed Genome Sequencer 20 system (454 Life Sciences) sequenced the 16S rDNA variable region to classify microorganisms, and carried out specific PCR (polymerase chain reaction, Polymerase Chain Reaction) on the 16S variable region by designing specific universal primers, and then used 454 sequencer sequencing, the phylogenetic tree based on this method shows good biodiversity, but its sequencing cost is high, although it is 1 / 10 of the cost of traditional capillary sequencing, it is the cost of other next-generation sequencers About 10 times the cost of sequencing

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