Although cultivation necessarily introduces bias in the specific taxa that are recovered, and thus cannot replace metagenomic methods for understanding microbial communities, it offers a few clear advantages. In principle, cultivation offers a much more robust way to explore genomic variation within populations. Mobile DNA elements, especially plasmids, are even more difficult to place in a metagenomic context.

Community metagenome sequencing can rapidly generate massive quantities of data from a microbiome, but with only limited ability to link genetic changes within the same genome or in populations of closely related cells. īut despite the tremendous advances in sequencing technology in the past decades, the paired phenomena of within-species strain diversity and between-species horizontal gene transfer still present a challenge to assessing the genetic structure of populations within diverse metagenomes like the mammalian gut. Understanding how genetic variation arises and changes within these communities is critical if we hope to develop useful models of their evolution.

Microbiota are complex mixtures of organisms, with dozens to hundreds of microbial species sharing genes both through ancestry with closely related strains, as well as through horizontal transfer to distantly related lineages.

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