Early metagenomic research proposed that many environments have groups of microorganisms that can’t be cultured or sequenced. There was abundant evidence to suggest that most organisms on Earth are comprised of these uncultured microorganisms. Thus, researchers began to conduct direct genetic analyses of the genomes of environmental samples.
They began cloning DNA from the environment and later screened it to discover how the genes expressed themselves functionally. Eventually, metagenomic next-generation sequencing (NGS) was applied to these microorganisms, and this allowed them to study these complex species without needing to isolate or cultivate a species within the confines of a laboratory.