I am using AMPure XP beads for a quick and crude way of purifying DNA from bacterial isolates. This method has been working quite well with a variety of bacterial cells (both gram positive and negative) but I have recently observed an odd phenomenon with bifidobacterium isolates.

The isolates are isolated from stool samples and selected and cultured in TOS media. The cell pellets washed 3 times with 1X PBS. Cells are lysed with lysozyme as well as Buffer AL (Qiagen) and also treated with Proteinase K. The mixture was clear after all these treatment.

AMPure XP beads are added to the lysate and resuspended well. The problem arises when the mixture is placed on the magnetic plate. The magnetic beads do migrate to where the magnet bar is, but they are not compacted and the magnetism is not strong. They also appear fuzzy and maybe, precipitated? If you were to tilt the tube, the magnet beads would flow with the solution. As such, I am unable to remove the supernatant without sucking up any beads. This is also true during the ethanol washes and during elution.

I have separately tested all my reagents and couldn't find the source to this phenomenon. I have also used another brand of magnetic beads and I observed the same thing. It all points to the sample, i.e. Bifidobacterium. Has anyone ever observed this phenomenon before and how do you solve this?

Any help is greatly appreciated.

Thank you!