Micro-filtration is a standard process for sterilization in scientific research, medical, and industrial applications, and to remove particles in drinking water or wastewater treatment. It is generally assumed, and confirmed by quantifying filtration efficiency by plating, that filters with a 0.1-0.45 microm pore size can retain bacteria. In contrast to this assumption, we have regularly observed the passage of a significant fraction of natural freshwater bacterial communities through 0.45, 0.22, and 0.1 microm pore size filters. Flow cytometry and a regrowth assay were applied in the present study to quantify and cultivate filterable bacteria. Here we show for the first time a systematic quantification of their filterability, especially their ability to pass through 0.1 microm pore size filters. The filtered bacteria were subsequently able to grow on natural assimilable organic carbon (AOC) with specific growth rates up to 0.47 h(-1). We were able to enrich bacteria communities that pass preferentially through all three pore size filters at significantly increased percentages using successive filtration-regrowth cycles. In all instances, the dominant microbial populations comprised slender spirillum-shaped Hylemonella gracilis strains, suggesting shape-dependent selection during the filtration process. This quantification of the omnipresence of microfilterable bacterial in natural freshwater and their regrowth characteristics demand a change in the sterile filtration practice used in industrial and engineering applications as well as scientific research.