Mar 9, 2026
If you are experiencing chronic infection, such as a recurrent urinary tract infection (UTI), non-healing wound, or another persistent condition, you may have heard about biofilms. You may have also heard about “biofilm disruptors” in patient support groups, forums, or from your doctor. Before taking this type of medication, it’s key to understand its relation to biofilms and impact to our microbial DNA testing.
Biofilms are a major reason why some infections resist standard antibiotic treatments and are difficult to properly diagnose with only traditional culture testing. They act as a protective shield for many bacteria and fungi, making them harder to detect and eradicate. Naturally, patients want to do everything possible to break them down, including taking biofilm disruptor supplements as soon as they are able.
However, if you are planning to use MicroGenDX’s Next-Generation DNA Sequencing (NGS) testing, when you intend to use a biofilm disruptor matters.
Using certain bacterial biofilm disruptors before you provide your sample can backfire, potentially leading to a false-negative or incomplete result.
Here is why you should wait until after your sample collection to start these products.
We recently received an important question from the patient community: Should I use a biofilm disruptor before my MicroGenDX test to "release" the bacteria?
Nick Sanford, PHD, our VP of Clinical Affairs, recommends:
We have not tested most biofilm disruptor compounds to determine if they interfere with our DNA extraction process. We strongly recommend avoiding any products containing DNase as these degrade the bacterial DNA we are attempting to detect.
Once test results are available, your healthcare provider can determine if biofilm disruptor therapy is appropriate for your specific clinical situation.
This guidance may seem counterintuitive. If biofilms hide bacteria, shouldn’t we break them open to find the bugs?
To understand why this is risky for DNA testing, we need to dive into the science of biofilms and how our testing works.
A biofilm is not just a random clump of bacteria. It is a sophisticated, structured community of microorganisms that attach to a surface and to each other. These communities stick together with strong adhesion and surround themselves with a protective slime layer. The vast majority of biofilms are beneficial to your body’s normal functions. They are present all over the body, living on surfaces in the gut microbiome, lungs, urinary tract, and more.
When free-floating (planktonic) bacteria enter your body, your immune system or antibiotics can often kill them easily. But when they attach to a surface, like the bladder wall, a prosthetic joint, or wound tissue, they undergo a radical change. They begin to secrete a slimy, glue-like substance called the Extracellular Polymeric Substance (EPS) matrix, also known as an extracellular matrix.
It is the EPS, the protective slime layer, that shields them from your immune system and standard testing, while heightening their resistance to antibiotics.
This extracellular matrix is composed of:
Think of this matrix as a walled fortress.
It physically blocks antibodies and white blood cells from reaching the bacteria and makes them difficult to detect via standard culture tests. It can also stop antibiotics from penetrating deep enough to kill the colony. Inside this fortress, bacteria can "talk" to each other (a process called quorum sensing), share antibiotic resistance genes, and even go into a dormant "sleeper" state where they are immune to many drugs.
In fact, research is showing that biofilms are commonly involved in 65% to 80% of all microbial infections in the human body, including long-term recurrent UTIs and chronic wounds.
Biofilm disruptors is a broad term for agents that attack this protective fortress. They work in different ways depending on their ingredients:
It is the latter two categories, but mainly the third category, DNase, that can pose a critical problem for DNA-based diagnostics like Next-Generation DNA Sequencing (NGS).
You might wonder: Why is there DNA outside the bacteria in the biofilm slime?
Bacteria release strands of their own DNA into the biofilm matrix to act as a structural scaffold like steel rebar in concrete. This extracellular DNA (eDNA) helps glue the biofilm together and enables the bacteria to exchange genetic information.
Because eDNA is such a critical structural component, enzymes that destroy DNA (DNase) are very effective at breaking up young biofilms. They literally dissolve the glue that holds the community together.
Side note: This exchange of DNA between bacteria is why MicroGenDX KEY tests include a PCR panel that detects antibiotic resistance genes present in the microbiota. Ultimately, this gives your provider a more complete picture of what treatments may or may not work against the specific microbes in your infection.
This is where the science of treatment clashes with the science of molecular diagnostics. Our lab uses both qPCR and Next-Generation DNA Sequencing (NGS) to support your provider's infection diagnosis. Unlike a standard culture, which tries to grow bacteria in a petri dish, both methods look for the unique genetic fingerprints (DNA) of the microbes in a sample.
qPCR detects 17 antimicrobial resistance genes and a specific panel of microbes, while NGS broadly screens the sample’s DNA fragments to identify organisms against our database of 60,000+ pathogens.
At a high level, the combined process looks like:
1. We extract bacterial DNA from your sample (urine, swab, etc.).
2. We use qPCR (Polymerase Chain Reaction) to amplify specific target genes, like the 16S rRNA gene, a key bacterial identifier. This is a separate, targeted detection method run alongside NGS.
3. We sequence DNA fragments via NGS to identify exactly which microbes are present —with 99.2% accuracy.
Here is the problem: If you take a biofilm disruptor containing DNase (or similar nucleases) right before your test, that enzyme doesn't just attack the biofilm's structural DNA.
If you take a biofilm disruptor containing DNase (or similar nucleases) right before your test, that enzyme doesn't just attack the biofilm's structural DNA. During the extraction process, any remaining DNase can degrade bacterial DNA once their cells are broken open—including the target genes, like 16S rRNA, that our technology relies on to identify microbial species.
If this genomic DNA in your sample is broken up by a disruptor before it reaches our lab:
As Nick Sanford noted, "We strongly recommend avoiding any products containing DNase as these degrade the bacterial DNA we are attempting to detect."
You might ask, "What if my disruptor doesn't list DNase?"
While DNase is the most direct threat to our test, other disruptors can still make an impact that is difficult to predict.
A common myth in patient communities is that you must break the biofilm to "release" bacteria into the urine or wound fluid so they can be detected.
While this logic applies to traditional cultures (which need live, bacteria to grow), it is less critical for DNA sequencing.
To ensure you get the most accurate, most complete, actionable answers from your MicroGenDX test, be sure to ask and follow your provider’s advice. However, a generic protocol may work:
Biofilm disruptors are powerful tools in the treatment of chronic infections, and we support their appropriate use under medical supervision. However, they can interfere with the molecular testing process, making the results less reliable for precision diagnosis and treatment.
You wouldn't use an eraser on a page you are trying to read. Similarly, avoid using DNA-destroying enzymes like DNase on an infection before letting our DNA-sequencing technology do its work to support your diagnosis.
Once you have results in hand, then it is best to discuss potential supplements with your doctor as they make their diagnosis and prescribe treatment.
Disclaimer: This information is for educational purposes only and is not medical advice. MicroGenDX is not a licensed medical provider and cannot give health advice. Do not start, stop, or change any medications without consulting your healthcare provider.
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