What is metagenomics?

Metagenomics is an approach commonly used to study the structure and function of microbiomes, which are the communities of microorganisms present in specific environments. In the context of AMR, metagenomics allows researchers to investigate how resistance emerges within a microbiome, and monitor how it spreads among the different microorganisms present.

The method involves isolating and sequencing all of the genetic material (DNA and RNA) present in a sample taken from an environment, and then assembling the reads into metagenome-assembled genomes, or MAGs, ready for further analysis. Some of the benefits of performing metagenomic analysis include: 

• Culture independent – Since metagenomics uses samples directly from the environment it is a culture independent approach, enabling all microorganisms to be studied, even those that are difficult or impossible to grow in the lab. 
• Holistic insights – Metagenomics enables researchers to investigate the entire microbial community at once and gain insights into species composition and diversity. Additionally by studying all of the microorganisms present, metagenomics can help to uncover interactions occurring between the different organisms within the community, as well as those occurring between the organisms and their environment. 
• Discovery of novel microorganisms and genes – By capturing all of the genetic material present in a sample it is possible to discover novel microbial species, metabolic pathways, and genes; some which may generate potentially useful products such as antibiotics, enzymes, or bioactive compounds. 

In the next section we will introduce you to the EMBL-EBI resource MGnify, which is used for the analysis and archiving of microbiome data.