Metagenomics

Metagenomics analyzes DNA extracted straight from an environmental or clinical sample rather than from a single organism grown in the laboratory. Classic microbiology depends on pure cultures, but most bacteria, archaea and microscopic eukaryotes have never been cultured, so much of microbial life went unseen until researchers began sequencing the mixed DNA of whole communities. The combined genomes present in a sample are called its metagenome.

Two main approaches are used. Amplicon sequencing copies and reads a single marker gene, usually the gene for 16S ribosomal RNA in bacteria and archaea, to list which groups are present and in what proportions. Shotgun metagenomics sequences random fragments of all the DNA; bioinformatics tools then sort the reads by organism, reconstruct partial or complete genomes and predict which genes, and so which abilities, such as antibiotic resistance or nitrogen fixation, the community carries.

Metagenomics has charted the human microbiome of the gut, skin and mouth, uncovered new species and genes in oceans and soils, shown how pollutants change microbial ecosystems and supplied enzymes for industry. In medicine, metagenomic sequencing of a patient sample can identify an infecting microbe without first having to grow it.