Most investigations of geographical within-species differences are limited to focusing on a
single species. Here, we investigate global differences for multiple bacterial species using a
dataset of 757 metagenomics sewage samples from 101 countries worldwide. The withinspecies
variations were determined by performing genome reconstructions, and the analyses
were expanded by gene focused approaches. Applying these methods, we recovered 3353
near complete (NC) metagenome assembled genomes (MAGs) encompassing 1439 different
MAG species and found that within-species genomic variation was in 36% of the investigated
species (12/33) coherent with regional separation. Additionally, we found that variation of
organelle genes correlated less with geography compared to metabolic and membrane genes,
suggesting that the global differences of these species are caused by regional environmental
selection rather than dissemination limitations. From the combination of the large and
globally distributed dataset and in-depth analysis, we present a wide investigation of global
within-species phylogeny of sewage bacteria. The global differences found here emphasize
the need for worldwide data sets when making global conclusions.