The only thing protecting a free-floating microorganism from the outside world is its cell wall. Cell walls are very important for letting good stuff (from the organism’s perspective) inside, and expelling the garbage.
As soon as that microorganism comes in contact with a surface, though, it can attach to the surface and generate a shell made up of extracellular polymeric substance (EPS—mostly complex sugars and some proteins) on top of itself, as an extra layer of protection. This is a biofilm. In addition to EPS, biofilms usually contain extracellular DNA as well.
Other organisms under the same biofilm can form a community, sort of the way humans group together in cities to pool their resources and cooperate for the mutual benefit of all. They can even recruit other organisms to join their communities, and they continue to undergo cell division as well. One major benefit of sticking together is that biofilms confer a much greater resistance to antibiotics.
Dental plaque is a well understood example of this in the body. These biofilms contain multiple species of organisms, both bacteria and fungi. Because we have direct access to dental plaque, we can bust up the biofilm physically: with brushing, or with dental tools.
Biofilms Inside the Body
Unfortunately, not all biofilms are so readily accessible. Biofilms play a role in a wide variety of infections (this NIH grant estimates as much as 80%). Biofilms are definitely a possible cause to consider for recurrent infections that just won’t go away.
One interesting approach to destroying biofilms involves Nitric Oxide (NO) donors. NO is used as a signaling molecule in the body, and also a vasodilator (it causes blood vessels to expand). This study showed that the addition of an NO donor dramatically increased the efficacy of antibiotic treatments on a biofilm of pseudomonas. NO donors have since been evaluated more generally, and in this study were shown to break down biofilms by about 63%, improving antimicrobial treatments 20-fold. (While the NO donors used in these studies are not available at this time as supplements, this makes me wonder about the amino acid arginine, which is also an NO donor and is mentioned in this study as a possible biofilm treatment.)
The best known treatments for biofilms, though, involve enzymes. Think of enzymes as very specific scissors, with an affinity for a particular substance. The enzymes that help you digest your food break down protein, carbohydrates, or fat; in the same way, enzymes taken away from food help to break up those sugars and protein and DNA in a biofilm.
If you’ve struggled with a chronic bacterial or fungal infection that either recurs or refuses to abate with what ought to be adequate treatment, consider asking your doctor about using systemic enzymes, away from food, in order to expose organisms that might be hiding from your immune system.