Research On Construction Methods Of Gene Catalogue Of Metagenome And Their Application

Metagenomics is a discipline that studies all microbial genomes in the environment.Its main research contents include the functions of various microbial species and various genetic resources in the environment,in order to promote the healthy growth of host or exploit functional microbial genes having benefit for production practice through changing the proportion of various microorganisms.Based on previous studies,this study used public databases,open source bioinformatics software and self-written programs in C/C++ and perl programming language to establish a complete pipeline for metagenomic gene set construction.Compared to published pipelines,our pipeline performed more rigorous filtering and checking on the sequencing reads data before metagenomic assembly,and for the first time introduced k-mer assisted analysis to evaluate the assembly accuracy,thus promoted the following assembly accuracy and gene prediction accuracy.The process is not fixed,and appropriate intermediate analysis steps can be used depending on the amount of data in the research project to save computing resources while obtaining correct biological conclusions.Among them,for the assembly process that occupies the largest memory,we have tried a variety of assembly strategies.By comparing,we have identified the advantages and disadvantages of various strategies and their application scenarios.The process is universal and can be used for different animal and plant or environmental metagenomic analyses.Applying this method to the Chicken Intestinal Metagenomics Project,we constructed the first complete gene set of chicken gut microbes.The completeness of the gene set is comparable to that of humans,pigs,and the like.In addition,based on this gene set,we systematically studied the effects of Macleaya cordata(a flowering plant)extract and a commonly used antibiotic,chlortetracycline,on the intestinal microbial community of chickens.This study of the gut microbiome has deepened our understanding of the promotion of animal growth by different feed additives.Applying this method to the invasive animal snail,Pomacea canaliculata,metagenome project,we constructed the first snail's metagenomic gene set.The microbial functional genes concentrated in the gene catalogue play an important role in the detoxification of the snail in the stress of heavy metal pollution,and the gene catalogue is an important supplement to the genomic function of the snail.In this project,some of the steps in the pipeline were adjusted to obtain a more complete set of genes.Although this process has the feasibility and correctness of the practice test,sequencing technology is changing with each passing day,and the algorithm research is advancing.In order to carry out more in-depth research on the microbial genomic information of a community,we need to update some of the steps.At the same time,as the amount of data increases,the increase in analysis speed is also an important task.In the future,we will continue to optimize the algorithms and speed up the programs.