Culturing and Preparing Bacteria
Using good aseptic culturing technique, grow cells in liquid culture or on agar plates until solid cultures are dense or liquid cultures are in early stationary phase. In practice, this would be equivalent of shaking a bacterial culture overnight or letting cells grow on a plate for 1-2 days. For agar cultures, growing cells on slants (glass tubes) may be more practical as it omits the centrifugation step below. However, liquid cultures normally yield a greater number of viable cells.
For liquid cultures, the cells are centrifuged, the culture broth is removed, and the pellet is suspended in an equal volume of lyophilization medium. We recommend Reagent 18 or the Microbial Freeze Drying Buffer, though skim milk and sucrose will work. For agar cultures, flood the plate/tube with 5-10 ml of lyophilization medium. Using a sterile pipette, flush the medium over the colonies to dislodge the cells. Transfer the cell suspension to a sterile tube. We recommend that a cell count is performed which can be compared to cells following freeze drying. A simple dilution to extinction protocol is available here.
Aliquot the cell suspension into sterile vials or tubes. Only 250-500 μl is needed per vial as this represents around 108 bacteria. Place split stoppers on the vials or loosely plug tubes with glass wool. Vials with split stoppers are technically open to the air, thus at risk of contamination. In practice we have not found this to be an issue. If a vial contains upwards of a billion bacteria, one or two contaminating microbes become insignificant when that culture is rehydrated and streaked. If there is fear of contamination, or containment, then glass wool or cotton can be placed under the stopper to prevent contamination.
Freeze Drying Process - Shelf Lyophilizer
Turn on the lyophilizer and start the condenser. If there is an external condenser using a dry ice/ethanol mixture then prepare this as well. The shelf can be set to 4°C.
Center the vials on the shelf. This placement is important so that the stoppering plate can evenly press on the stoppers following freeze drying.
Using either manual or programmed controls, freeze the samples down to -40°C. This step should take approximately 30-60 minutes and is very dependent upon the instrument. If the rate of freezing can be controlled, then a drop of 1°C per minute is a practical rate. Once the samples reach temperature, they should be visibly frozen (clear liquid turn opaque and skim milk appears solid).
Allow the sample to sit at -40°C for 1 hr to ensure complete freezing. Vials at the center of a cluster may freeze more slowly than those on the outside.
Turn on the vacuum pump. Within 10-20 minutes, the vacuum should be under 200 millitorr (mtorr). Depending on the instrument, pressure may be reported in mtorr, mbar, Pascal, or "inches Hg" on a vacuum gauge. For reference, 100 mtorr = 0.133 mbar = 13.3 Pascal = 29.9" Hg = 0.000132 atm = 99.99% vacuum.
Once the vacuum is below 200 mtorr, increase the temperature of the shelf for primary drying, the phase associated with water sublimation. The temperature of the shelf is dependent upon the lyophilization medium. For sucrose, keep the shelf temperature at -25°C. For Reagent 18 or Microbial Freeze Drying Buffer, the shelf can be as high as -15°C. In any case, the greater the difference in temperature between the shelf and the condenser/ice trap, the more efficient the primary drying process will be.
If melting of the samples occurs, then it might be necessary to empirically determine a shelf temperature. A practical means to do this involves placing a sample of the lyoprotective medium on a shelf and incrementally lowering the temperature every 15 minutes. At some point the sample freezes. Under vacuum with a cold trap, your sample will be safe and will remain frozen. This is a practical method and is certainly not necessarily the most efficient primary drying temperature, but it should work well enough.
Primary drying is the longest phase of the freeze drying process. The idea is to keep the sample colder than condenser (or ice trap) but still sufficiently warm so that water sublimes rapidly. The temperature of the shelf can be raised to above the melting temperature as long as the sublimation process removes the heat flowing into the sample sufficiently fast to prevent melting and sample collapse (where the matrix literally caves in). The time for primary drying will also depend upon the volume of the sample. For bacteria, samples rarely need to be large and typically are 0.25 to 0.5 ml. A limited number of samples (10-20) in a shelf dryer can be completed in just a couple of hours. A fully loaded dryer with several hundred samples will take longer. Safely, a primary drying period which is overnight should work, but test this first before you attempt to freeze dry large numbers of vials. As a standard guide, freeze dry overnight.
Samples still contain moisture following primary drying. The amount is debatable, but it somewhere between 2 and 4%. This moisture level needs to be reduced and that is done by pumping heat into the sample during the secondary drying phase. This phase is relatively short, lasting 1 to 2 hours, but important for long-term viability. However, over drying of the bacteria can be detrimental as well. Once again, based on the idiosyncrasies of your lyophilizer and samples, the ideal time for secondary drying needs to be determined experimentally. Generally, raise the shelf temperature to 20°C and dry for 2 hours.
With the vacuum in place, stopper the vials using the stoppering plate/mechanism. Release the vacuum, remove the vials, and further secure the rubber bungs/stoppers with foil crimp seals. It is best to store the vials at 4°C in the dark.
Test the freeze dried bacteria for viability as compared to the original culture (see link). Additionally, monitor the stability/viability of the freeze dried cultures by testing at 30, 90, 180 and 365 days. A good protocol will yield nearly 100% viable cells. Anything above 50% is considered acceptable by many labs. Skim milk will yield 10-20%. However, % viable after freeze drying is not as important as the number viable following storage. If viability starts to decline rapidly by a log or more per month, then modification of the protocol is probably necessary. Note that some strains are simply very difficult to freeze dry and no matter what, these may die off quickly following lyophilization.