Disaggregate with surfactant

Surfactants like TWEEN® 20 and TWEEN® 80 may disperse the bacteria which prevents aggregation. Enzymes like DNase may also be effective to disaggregate some types of bacterial clumps.

In either case, add surfactant to your sample and then disaggregate mechanically afterwards.

Avoid high concentrations

Schematic view of a micelle. By SuperManu - Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=2902736

Avoid high surfactant concentrations since this may lead to the formation of large, aggregate micelles. BactoBox® may count and classify the micelles, which leads to surprising results.

At high concentrations these soap bubbles may completely dwarf the concentration of intact cells. E.g. if the concentration of aggregate micelles is more than 1000 times higher than intact cells. In such a case, it is virtually impossible to find a dilution factor that results in an actual number for intact cell concentrations.

Even at lower concentrations, micelles may surprise you when you look at the BactoBox® results. Typically, aggregate micelles appear as a population centered at approximately 1 rad in the HF phase dimension. This may lead to the false impression of a low cell percentage if the gating classifies them as other. You can subtract these objects from the result in post analysis but bubble concentration is still important during analysis because it contributes to detector saturation (e.g., the total/mL concentration).