In the reporting period, we were able to achieve many of the envisioned tools and applications of the proposal. Regarding tool developments, we have published a single nucleotide analyser, metaSNV (Costea et al., PlosOne2017), devised methods for gene content analyses of conspecific strains, subspecies delineation protocols (Costea et al., Mol. Sys. Biol. 2017) and many other analysis tools and resources that are required to zoom into strain resolution (e.g. the bacterial genome resource proGenomes: Mende et al., NAR 2017; an update of our eggnog (meta)genome annotation resource: Huerta-Cepas et al., NAR 2017; and a tool to annotate newly sequenced (meta)genomes: Huerta-Cepas et al., Mol. Biol. Evol.2017). Regarding the identification of known strains in metagenomics data, we have developed a respective pipeline that we are still testing and investigated the transmission or oral strains into the gut. We analysed longitudinal data using SNV markers (Li et al., Science, 2016; Korpela et al., Genome Res. 2018, in press), although we continue to refine the results. Finally, we have identified and quantified subspecies in the vast majority of abundant and prevalent human gut microbes, which have a distinct biogeography and which seem to be exclusive and stay with the host for a long time (Costea et al., Mol. Sys. Biol. 2017). We also zoomed beyond the species level in disease applications (e.g. in colon cancer, unpublished) or for Parkinson’s disease (Bedarf et al., Genome Med. 2017) and pointed to the need of strain level resolution in metagenomics (Schmidt et al., Cell 2018).