Bacterial Cell Disruption by Bead Beating

Bacteria can be easily disrupted by treatment with enzymes and detergents.  For gram positive organisms, removing the cell wall and then lysis by the addition of SDS or similar detergent are suitably early steps in isolating nucleic acids.  Gram negative organisms, such as E. coli, simply require exposure to SDS to lysis.  Enzymes and/or detergents are useful if nucleic acids are the target.  If proteins or cellular components are sought, then alternative methods must be used.   Bead beating and sonication are both proven alternative techniques to disrupt bacteria.

Small beads are the most effective for cracking bacteria.  Typically 100 µm zirconium or silica beads are the most effective for disrupting bacteria. For dilute bacteria, low binding beads will provide high yields of analytes, thus improving assay sensitivity.

Protocol - General Parameters

  1. Bead beating bacteria can be performed in microfuge tubes, deep well plates, 4 ml vials, 15 ml vials, or in customized 125 ml jars for batch processing.  Regardless of the container, it is important to not to overfill with both beads and culture.  Generally the container should not be more than half full of beads and bacterial sample.  Of that, 1/3 should be beads and 2/3 sample.  Thus, in a 2 ml microfuge tube, roughly 350 µl should be beads and 650 µl sample.  It is important that the beads and bacteria have head space to move in during beating, thus no detergents should be added during processing.
  2. Depending upon the application, bacteria can be homogenized in culture medium or centrifuged and resuspended in a suitable homogenization/lysis buffer.  Prepare cells and add to pre-filled microfuge tubes or other tubes or plates containing beads.  Tubes and plates should be "loaded" with beads before the sample is added.  A small scoop which is approximately 300 µl can be used to load tubes quickly.  Plates can be loaded using a scoop and small funnel to load individual wells.  Custom tube and plate fillers are also available to load racks of tubes and plates more rapidly.
  3. Cap the tubes/plates with closures that do not leak.  For screw cap microfuge tubes, be certain to use caps with "O" rings.  For plates, tight fitting polypropylene strip caps are recommended.  With strip caps, each well is sealed with an individual cap.  Silicone press on mats have been found not to work well with high throughput bead beating as they tend to leak and cause cross contamination.
  4. Individual tubes can be processed in a Pulsing Vortex Mixer effectively.  For full racks of tubes or plates, then a high throughput homogenizer is needed.  Both the Geno/Grinder and HT Homogenizer are very effective at homogenizing large number of bacterial samples.  For a basic homogenization procedure, place the samples in the homogenizer and process for 5 minutes on high speed.
  5. Optimizing the homogenization process requires beating the sample for short durations and then assessing the degree of disruption at each time point.  The release of the enzyme lactate dehydrogenase from disrupted cells is a parameter successfully used to measure homogenization efficiency in many different biological samples.  For bacteria, prepare at least six microfuge tubes with cells and beads (ideally it would best to run this test in triplicate, thus 18 tubes would be better if space allows in the homogenizer).  Start by removing a tube before processing and labeling it 0 min.  Run the homogenizer for 2 minutes, stop and remove a sample(s) and label.  Restart the homogenizer and repeat the process removing samples at 4, 6, 8, and 10 minutes.  Label all tubes accordingly.
  6. Pellet the bacterial cells and debris by centrifugation.  Test the supernatant for lactate dehydrogenase (LDH) activity using a commercially available test kit or standard LDH assay protocol (link).  The tube with the highest enzyme activity or where the activity peaks with the least processing represents the optimal processing time.  Note that LDH is only one of many possible cellular enzymes that can be used for assessing cell disruption.