Method for analyzing microbial population function by using metagenome data
A metagenomic and microbial technology, applied in the field of microbial population function analysis using metagenomic data, can solve problems such as unreliability, increase the difficulty of integrated databases, and inability to splicing, and achieve improved utilization, excellent universality and information. comprehensive effect
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[0063] Example 1 Construction of Microbial Metagenomic Reference Database
[0064] This embodiment takes NCBI and KEGG as the target biological information database. Those skilled in the art can choose other biological information databases in the field to use the method of the present invention to construct a microbial metagenomic reference database. These choices are all conventional choices based on the inventive concept of this application, and therefore do not exceed this application. The scope of protection.
[0065] 1. Download the whole genome sequence of all microorganisms from different sources and different types in NCBI. The data obtained is a .fna file, which includes the NC number, base sequence, gi number and corresponding species information of the whole genome sequence.
[0066] 2. Download the .gbk annotation files of all microorganisms in NCBI, and extract the classification information of related species from the .gbk annotation files based on the NC number and ...
Example Embodiment
[0073] Example 2 Method of using metagenomic data to analyze microbial population function
[0074] 1. Sequencing the metagenomics of the microbial population to be tested and quality control of the sequencing data: remove the bases with a sequencing quality value of less than 20, further remove sequences with reads less than 25bp in length, and remove reads from the host DNA to reduce Errors that may occur during sample extraction and sequencing, resulting in high-quality whole-genome sequencing data.
[0075] 2. Species abundance calculation: compare the microbial species data set in the microbial metagenomic reference database constructed in Example 1 of the high-quality reads obtained in step 1, and calculate the species abundance to obtain the data Abundance values of all species. Based on the species abundance value, the difference analysis of various microbial compositions between different samples is carried out.
[0076] 3. Gene abundance calculation: compare the high-qu...
Example Embodiment
[0078] Example 3 Microbial population functional metagenomic analysis of poultry intestinal contents in a small sample amount
[0079] In this embodiment, the metagenomic data of the intestinal contents of individuals in the health and disease groups of a small sample of poultry were sequenced and analyzed. The experimental subjects used were 18 individual poultry individuals from the same industrial farm, divided into two groups with 9 samples in each group; among them, the disease test group was an individual who had been diagnosed with avian colibacillosis by a veterinarian. The group is healthy individuals.
[0080] Through microbial whole-genome shotgun sequencing, metagenomic sequencing was performed on the DNA extracted from the above 18 intestinal contents samples. Then, the method for analyzing the function of the microbial population using metagenomic data established in Example 2 of the present invention and the existing conventional method (the method introduced in the...
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