 Metagenomics (also referred to as ‘environmental’ or ‘community’ genomics) is a research field that aims to analyse the collective genomes of microbial communities. These communities are usually extracted from environmental samples, ranging from soil to water or even air samples. A major advantage of metagenomics is that it does not rely on techniques for culturing microbes. This is important because only an estimated 1%–5% of all microbes can be cultured at all (Amann et al. 1995), an issue that has been referred to as the ‘great plate count anomaly’ (Staley &amp; Konopka  1985).[23]