Molecular Microbiology Research 2024, Vol.14, No.1, 20-30 http://microbescipublisher.com/index.php/mmr 21 1 Metagenomics Technology and Its Application in Environmental Microbial Research 1.1 Principles of metagenomics technology Metagenomics, this cutting-edge branch of biology, focuses on revealing the genetic information of all microorganisms in environmental samples, in contrast to traditional genomics, which focuses solely on a single species. Goussarov et al. (2022) focused on the principles and methods of recovering metagenomic assembled genomes from metagenomic data, emphasizing the workflow from DNA sequencing to functional annotation. Its research begins with the collection of environmental samples, which may originate from multiple environments such as soil, water, air or inside organisms. After pretreatment such as filtration and centrifugation, cells are disrupted using physical or chemical methods to release DNA. Subsequently, the DNA is extracted and purified to remove impurities and RNA. The DNA fragments need to be further constructed into libraries and sequenced. Library construction is to connect DNA fragments to vectors to form a sequenceable DNA library. Sequencing uses second- or third-generation high-throughput sequencing technology to conduct massively parallel sequencing of DNA fragments in the library. Garrido-Cardenas et al. (2017) describe metagenomics as a set of techniques for analyzing microbial communities that can be isolated from a specific environment without culturing. This involves large-scale sequencing, or next-generation sequencing, because of the difficulties traditional methods present when trying to transfer all the microorganisms present in a given environment into the laboratory. Hiraoka et al. (2016) found that bioinformatics analysis makes it possible to mine huge metagenomic data sets and discover general patterns that control microbial ecosystems. Metagenomic approaches will allow us to move beyond routine analyses, broaden our understanding of microbial ecosystems, enrich reference databases, and develop more powerful biological information. The raw data generated by sequencing is rich in genetic information and needs to be transformed into useful information through bioinformatics analysis. This includes steps such as quality control, sequence assembly, and gene annotation. Quality control ensures data accuracy and reliability and removes low-quality data. Sequence assembly splices short fragments into longer sequences to form a draft genome or transcriptome. Gene annotation determines sequence function and origin by comparing it with known gene databases (Figure 1). Figure 1 Common analytical processes for metagenomic sequencing analysis (Peng et al., 2022) Metagenomics technology can reveal the species composition, gene types, functions and inter-species interactions of microbial communities in environmental samples. This information is critical to understanding the role of microorganisms in ecosystems and their interactions with environmental factors. Metagenomics provides new perspectives and methods for environmental microbial ecology research and promotes the development of this field.
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