Fig. 2

Single cell genomics [102]. In a nutshell, this approach starts with isolating single microbial cells, typically using fluorescence activated cell sorting (FACS) or microfluidics. Then, cells are lysed, and their genomic DNA is amplified, generating single amplified genomes (SAGs). SAGs are subsequently shotgun sequenced, and the produced reads (DNA sequences) are assembled and annotated. Those SAGs from the same species can then be used for population genomics analyses (as in Kashtan et al. [53, 98]). Furthermore, SAGs can be used as genomic templates in metagenome-based population genomics analyses [103] (Fig. 3)