Metagenomics

Article

May 21, 2022

Metagenomics is a field of microbiology and virology that deals with genomic DNA recovered directly from environmental samples. In a broad sense, it is also called environmental genomics, ecogenomics, or community genomics. It is also called Metagenomic analysis, or simply Metagenome. Conventional microbial genome analysis requires a process of separating and culturing a single strain from an environmental sample, but metagenomic analysis does not go through this process and extracts genomic DNA directly from the microbial community (bacterial flora). Then, DNA sequencing is performed with DNA derived from various strains mixed. Therefore, it is possible to obtain genomic information of microorganisms belonging to difficult-to-cultured / uncultured strains, which was difficult in the conventional method based on culture in metagenomic analysis. According to one theory, it is estimated that more than 99% of the bacteria living on the earth are strains that cannot be cultivated alone, and metagenomic analysis can elucidate a huge number of unknown bacteria and unknown genes buried in the environment. It is expected as a method. The cost of DNA sequencing is getting cheaper year by year, and it is expected that larger-scale and detailed metagenomic analysis research will be conducted. In a narrow sense, metagenomic analysis refers to the analysis of sequence information of the entire genome obtained by shotgun sequencing, and is distinguished from amplification sequences (such as 16S rRNA tag sequences) that have undergone PCR by narrowing down the target gene, but the latter. May be included in metagenomic analysis in a broad sense. Today, various indigenous bacterial flora such as seawater and soil, intestines and oral cavity, seafloor whalebone bacteria, biofilms in mine wastewater, animal and plant symbiotic bacteria, sewage treatment facilities, Antarctic ice sheets, hot springs, deep layers. Metagenomic analysis targeting various environments such as the crust has been reported as a paper.

Etymology

The term metagenomics was named by adding the word "meta" to the "genome" to represent higher dimensions. It is based on the idea that it is possible to collect and collectively (meta-) analyze the gene sequences of the genome from the environment, similar to studying the genome of a single organism. The term was first used in the paper in 1998 by Jo Handelsman, Jon Clardy, Robert M. Goodman, Sean F Brady and others. In 2005, Kevin Chen and Lior Pachter defined metagenomic analysis as "an application of modern genomics technology that does not require individual fungi to be isolated or cultured in the laboratory."

History and background

Traditional DNA sequencing initially required culturing a single bacterial strain. However, early metagenomic analysis studies have revealed that many environments have many microorganisms that cannot be cultivated and are difficult to sequence. These early studies focused on examining the 16S rRNA gene sequence. While this gene sequence is relatively short and highly conserved within prokaryotic species, changes are seen between different species, making it easier to systematically examine microbial communities in the environment than to sequence the entire genome. Can be done. DNA sequences of 16S rRNA gene sequences were performed on many environmental samples, and as a result, many sequences that did not fit into the known species being cultured were found. This indicates that there are extremely diverse uncultured strains of microorganisms in the environment. Is the 16S rRNA gene sequence in the environment without culturing in this way?