In the ninth episode of The Healing Terrain, Dr. Drew Kidder is joined by Dr. Emily Hernandez to explore biofilms and the role they may play in persistent or recurring infections.
Drawing on her experience working with complex chronic illness, Dr. Hernandez explains how biofilms form, the mechanisms that make them resilient, and why practitioners may need to look beyond simply adding another antimicrobial when a patient’s progress stalls.
What Is a Biofilm?
Dr. Hernandez described a biofilm as a structured community of microorganisms surrounded by a protective extracellular matrix.
“Basically, what it is, is a sticky matrix produced by microbes, often polymicrobial.”
These communities may contain one or multiple microbial species. The surrounding matrix helps them attach to a surface, exchange resources, communicate, and respond collectively to their environment.¹
“They form this kind of sticky matrix that they can hide behind. It creates this community where they can share resources, communicate, and survive.”
Rather than behaving as isolated, free-floating—or planktonic—organisms, microbes within a biofilm function as an organized community. This can make them more resilient than the same organisms would be on their own.
Not Every Biofilm Is Harmful
Dr. Hernandez emphasized that the presence of a biofilm is not automatically a sign of disease.
“Not all biofilm is bad, just like all microbes aren’t bad. We just want them in the right balance.”
Biofilms occur throughout nature and can be part of normal microbial ecosystems. The clinical concern is their potential involvement in infection, dysbiosis, or another harmful imbalance.
“The issue is not necessarily that all biofilm is bad. It’s: What are the actual microbes that are creating the biofilm? Have they become overgrown? Are they opportunistic?”
That distinction matters. The goal is not to eliminate every microorganism or biofilm, but to understand when a microbial community may be contributing to a patient’s condition.
Why Biofilms Can Be Difficult to Address
The biofilm matrix creates a physical barrier that may limit the penetration of antimicrobial agents. But the matrix is only one part of the biofilm’s defense.
Biofilm-associated microbes can alter their metabolism, communicate through signaling systems, exchange genetic material, and disperse to establish new communities. Together, these mechanisms can increase their tolerance to immune defenses and antimicrobial treatment.²
“They use multiple different mechanisms to protect themselves,” Dr. Hernandez explained. “First, it’s an actual physical barrier.”
She also described quorum sensing, a form of chemical communication microorganisms can use to coordinate group behavior.
“They use quorum sensing, which is how bacteria communicate and congregate together as a colony.”
Another mechanism involves efflux pumps—proteins that allow bacterial cells to expel certain compounds. Efflux activity is one of several factors that can contribute to antimicrobial resistance.³
“They have these little pumps found on their membrane that are responsible for pumping out whatever is threatening [them].”
Biofilms and Antimicrobial Resistance
Biofilms can create conditions that support the persistence and exchange of antimicrobial-resistance genes.⁴ This is one reason biofilm-associated infections can be especially challenging to manage.
Dr. Hernandez believes practitioners need to consider more than a single therapeutic mechanism.
“We need to make sure that we’re using multiple different mechanisms to address these different infections.”
That does not mean prescribed antibiotics should be avoided or discontinued. Antibiotics remain essential for treating many bacterial infections and should be used as directed. Instead, the conversation highlights the need for appropriate diagnosis, antimicrobial stewardship, and a strategy suited to the specific infection and patient.
When Practitioners May Consider Biofilms
There is no single general laboratory test that establishes biofilms as the cause of a patient’s symptoms.
“The reality is we don’t have any general test yet, at least, that can test for biofilm. So, you have to use your clinical reasoning.”
Biofilms are well documented in certain settings, including chronic wounds, implanted medical devices, and some persistent bacterial infections.⁵ Their possible role in an individual patient should be evaluated in the context of the diagnosed condition, medical history, testing, and response to treatment.
Dr. Hernandez said she becomes more curious about biofilms when an appropriately treated infection persists or recurs.
“What often we’ll see in clinical practice is that either people don’t get better, they have these recurring infections, or they may start to temporarily feel better—and then, as they come off their protocols, they start to have symptoms again.”
Symptoms such as fatigue, brain fog, gastrointestinal discomfort, and joint pain are not specific to biofilms and should not be used to diagnose one. They can, however, signal the need to look more closely at the patient’s overall clinical picture.
Why Starting With Biofilm Disruption May Backfire
Once a practitioner suspects biofilm involvement, the temptation may be to attack it aggressively. Dr. Hernandez cautioned against making biofilm disruption the first step.
“If you try to just break open biofilm with patients as your first step, your patients may get a little bit upset with you because they’re most likely going to feel a little bit worse.”
She favors a measured approach that considers the patient’s overall capacity and prepares the pathways involved in elimination.
“We want to go low and slow. We want to do this in the right order.”
New or worsening symptoms after starting a protocol should not automatically be assumed to be a “die-off” or Herxheimer reaction. The Jarisch-Herxheimer reaction is a specific inflammatory response associated primarily with antimicrobial treatment of certain spirochetal infections. Symptom changes may have many other causes, including an adverse reaction or progression of an illness, and should be evaluated by a qualified healthcare professional.
Drainage Before Deeper Support
Before introducing biofilm-focused support, Dr. Hernandez assesses the body’s ability to move and eliminate waste.
“First, I do want to work on drainage and detoxification. Make sure that these pathways are open so that the body can actually have somewhere to move the toxins.”
She distinguished drainage from detoxification in the same way Dr. Kidder did in Episode 7.
“Detoxification, we are mobilizing toxins. Drainage is—we’re just getting them out.”
Bowel regularity, hydration, urination, perspiration, liver and gallbladder function, and lymphatic movement may all be considered within this broader assessment.
“We have to make sure those general windows and doorways are open. Otherwise, if they’re not, those toxins get recirculated.”
Where Binders May Fit
Dr. Hernandez also incorporates binders before adding more targeted biofilm support.*
“I start all my patients off with some sort of binder before I add anything that’s biofilm-busting.”
She compared the strategy to placing police outside a jail before opening its doors: the goal is to have support in place before disrupting what is inside.
“I often use binders to help mop up and grab onto those toxins as we’re opening up the floodgates.”
A Multi-Mechanism Approach to Biofilms
Dr. Hernandez discussed her clinical experience using Biocidin®, a blend of 18 botanicals and essential oils, as part of her biofilm protocols.*
“I have been using [Biocidin] clinically for the 12 years I’ve been in practice.”
She described several mechanisms associated with individual botanicals in the formula, including support for microbial balance and effects on biofilm attachment, quorum sensing, motility, and efflux activity.*
“There are so many different herbs in it that all these mechanisms are working simultaneously to create this synergistic effect.”
Dr. Hernandez sees value in addressing biofilms from several directions instead of relying on a single “biofilm buster.” The appropriate approach, however, depends on the organism, location of the suspected biofilm, patient history, concurrent treatment, and strength of the available evidence.
How to Know When a Protocol Is Moving Too Quickly
Dr. Hernandez watches for symptoms that become noticeably worse after a patient introduces or increases an antimicrobial product.
“If they’re bloated, their bloating gets worse. If they’ve got headaches, their headache gets worse.”
When this happens, she reassesses the protocol rather than encouraging the patient to push through.
“Basically, what it means is that there is more burden on the body than the body can handle at that particular time.”
The appropriate response may include pausing or reducing a product, reviewing drainage and elimination, checking for interactions, and evaluating whether the symptoms represent an adverse effect or another medical issue. Patients should make these decisions with their healthcare practitioner rather than adjusting prescribed treatment independently.
Biofilm Support Takes Time
Dr. Hernandez reminded practitioners that a long-standing imbalance is unlikely to be resolved immediately.
“This didn’t happen overnight. This imbalance and this overgrowth—it’s going to take some time to get everything back into balance.”
She encourages practitioners to treat biofilm support as a gradual process rather than an aggressive event.
“Work on it low and slow. It’s just something that you’re doing in the background. It doesn’t have to be all at once.”
That measured approach gives the practitioner room to observe, adjust, and respond to what the patient’s body is communicating.
Listen to What Symptoms Are Communicating
Dr. Hernandez closed by reframing symptoms as information—not as automatic proof that a protocol is working or failing.
“Symptoms are a way that our body is communicating. It doesn’t mean things are good or bad, or not working or working.”
For practitioners, that means staying curious when a patient reacts. What changed? When did it begin? Is the intervention appropriate? Does the patient need a different pace, additional support, or further evaluation?
“No matter how complex your healing journey is—or your patients are—it really gets back to the basics and the foundation, and just peeling back the layers one at a time.”
Listen to the Full Episode
Biofilms and Why Infections Don’t Go Away is available on DrTalks, Apple Podcasts, Spotify, and YouTube.
References
- Nadell CD, Xavier JB, Foster KR. The sociobiology of biofilms. FEMS Microbiol Rev. 2009;33(1):206-224. doi:10.1111/j.1574-6976.2008.00150.x
- Flemming HC, Wingender J, Szewzyk U, Steinberg P, Rice SA, Kjelleberg S. Biofilms: an emergent form of bacterial life. Nat Rev Microbiol. 2016;14(9):563-575. doi:10.1038/nrmicro.2016.94
- Colclough AL, Alav I, Whittle EE, Pugh HL, Darby EM, Legood SW, et al. RND efflux pumps in Gram-negative bacteria: regulation, structure and role in antibiotic resistance. Future Microbiol. 2020;15:143-157. doi:10.2217/fmb-2019-0235
- Michaelis C, Grohmann E. Horizontal gene transfer of antibiotic resistance genes in biofilms. Antibiotics (Basel). 2023;12(2):328. doi:10.3390/antibiotics12020328
- Sahoo K, Meshram S. Biofilm formation in chronic infections: a comprehensive review of pathogenesis, clinical implications, and novel therapeutic approaches. Cureus. 2024;16(10):e70629. doi:10.7759/cureus.70629
*These statements have not been evaluated by the Food and Drug Administration. These products are not intended to diagnose, treat, cure, or prevent any disease. This content is for educational purposes only and is not a substitute for individualized medical advice, diagnosis, or treatment.
