We used FACS to isolate bacteria that were cultured from stool samples, and then selectively isolated using BONCAT-FACS. We had tubes with 500k, 1M, and 2.5M bacteria, and used the BiOstic Bacteremia DNA Isolation Kit, but did not get any results on DNA yield using Nanodrop or DNA amplification and visualising with EthBr.

What could explain low/no DNA yield, and what could be optimized?