In microbiological applications, it is often necessary to homogenize a sample in order to release bacteria or other single-celled organisms contained within the sample, and these organisms are often required to remain intact and viable for downstream analysis. This is an application which paddle blenders were specifically designed for, but other homogenizers may be sufficient as well if a very high microbial yield is not required.
Paddle blenders are also the tool of choice for extraction of viruses. However, due to the extremely small size of viruses, they are easier to extract and other homogenization technologies can be more effectively used as well.
If you will not need to use your homogenizer for other applications, and will be solely using it for microorganism extraction, a paddle blender is the correct choice. It will be far more efficient and provide a far higher yield of viable microorganisms than any other homogenizer technology.
If you are looking for a multi-purpose homogenizer, then a bead mill can do the trick as well. Be sure to select an instrument that has a very low minimum speed setting and use large beads, as these will effectively break apart the sample but will be less efficient at lysing cells.
Rotor-stators may be used, but are generally not recommended. If you already own a rotor-stator homogenizer, try operating it at the lowest speed, then if it does not disrupt the sample, slowly increase the speed until the sample is disrupted. Once the gross structure of the sample is disrupted and there are no more noticeable pieces of solid in the sample, stop homogenization.
Mortars and pestles are difficult to optimize due to reproducibility issues and are therefore not recommended. Never use ultrasonics for the extraction of intact microorganisms, as they disrupt cells highly efficiently.