Metagenomics

Metagenomics is the study of all genetic material from all organisms in a particular environment, providing insights into their composition, diversity, and functional potential. Metagenomics has allowed researchers to profile the microbial composition of environmental and clinical samples without the need for time-consuming culture of individual species.

Metagenomics has transformed microbial ecology and evolutionary biology by uncovering previously hidden biodiversity and metabolic capabilities. As the cost of DNA sequencing continues to decline, metagenomic studies now routinely profile hundreds to thousands of samples, enabling large-scale exploration of microbial communities and their roles in health and global ecosystems.^[2][3][4]

Metagenomic studies most commonly employ shotgun sequencing^[5] though long-read sequencing is being increasingly utilised as technologies advance.^[6] The field is also referred to as environmental genomics, ecogenomics, community genomics, or microbiomics and has significantly expanded the understanding of microbial life beyond what traditional cultivation-based methods can reveal.

Metagenomics is distinct from Amplicon sequencing, also referred to as Metabarcoding or PCR-based sequencing.^[7] The main difference is the underlying methodology, since metagenomics targets all DNA in a sample, while Amplicon sequencing amplifies and sequences one or multiple specific genes.^[8] Data utilisation also differs between these two approaches. Amplicon sequencing provides mainly community profiles detailing which taxa are present in an sample, whereas metagenomics also recovers encoded enzymes and pathways.^[9] Amplicon sequencing was frequently used in early environmental gene sequencing focused on assessing specific highly conserved marker genes, such as the 16S rRNA gene, to profile microbial diversity. These studies demonstrated that the vast majority of microbial biodiversity had been missed by cultivation-based methods.^[10]