Antimicrobial Agents: When and How They May Help Your Health

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Do you want to start feeling better?

Yes, Where Do I Start?

Antimicrobial Agents: When and How They May Help Your Health

How Antibacterial, Antifungal and Antiparasitic Agents Help Your Gut Heal

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Key Takeaways

  • Antimicrobial agents include a variety of plant and herbal extracts that can knock out bad bacteria and other infectious microbes.
  • They can help with stubborn cases of SIBO, dysbiosis and fungal or parasitic infections, and the effects of these, such as fatigue, inflammation and brain fog.
  • Antimicrobials are a useful extra nudge to balance gut health, but diet and probiotics should be the first lines of defense.
Antimicrobial agents: 3D illustration of a virus attacking blood cells

Dealing with crippling fatigue, brain fog, and inflammatory or autoimmune issues can be debilitating. 

These issues often originate in the gut and may occur due to imbalances in good and bad gut bacteria (dysbiosis), small intestinal bacterial overgrowth (SIBO), or increased permeability of the intestinal lining (“leaky gut”).

Some people can normalize gut microbial balance and restore resilience and integrity to their intestinal lining without the extra assistance of antimicrobial agents — in these people, diet, lifestyle and probiotics can be sufficient to restore balance and resolve symptoms.

But for others, antimicrobials can be a game changer. In this article, we’ll explore when and how to consider antimicrobial agents, what they do, and which ones have been shown to be the most effective.

What Are Antimicrobial Agents?

Antimicrobial agents: Common gut pathogens

Antimicrobials are substances that kill or prevent the growth of microbes. They include [1]:

  • Antibiotics (antibacterial agents) 
  • Antivirals
  • Antifungals
  • Antiprotozoals

Antibiotics vs. Antimicrobials

While all antibiotics are antimicrobials, not all antimicrobials are antibiotics [2].

Antibiotics are exclusively antibacterial. For example, most of us have either heard of or been prescribed antibiotics such as chloramphenicol, penicillin/cephalosporins, streptomycin, or tetracycline. You might also know of some common bacterial growths that antibiotics help eliminate — such as Escherichia coli (E. coli) and staphylococcus aureus.

However, antimicrobials combat a wider variety of microbes (microorganisms). Antimicrobial agents include not just bactericidal and bacteriostatic compounds that kill or inhibit bacteria but also those that have toxicity or inhibition against viruses and fungi, or which are antiparasitic.

When to Introduce Antimicrobials

Antimicrobial agents: 3 steps for gut health

Most of my patients who have issues such as brain fog, poor mood, autoimmune and inflammatory conditions are also dealing with imbalances within their gut microbiology. Such imbalances can include SIBO, fungal overgrowth (yeast or candida), H. pylori, and parasitic worms [3, 4, 5].

With this being the case, you may wonder why I don’t recommend antimicrobial agents as a first step for chronic symptoms related to poor gut health. 

The reason is that in a science-based approach, diet and probiotics should always be the first foundation to tackling gut health issues, with antimicrobials a third line option. 

This order doesn’t just come from my own experience with patients, but from research evidence and good practice guidelines around the world. For example, the 2021 IBS treatment guidelines from the British Society of Gastroenterology and Romanian Society of Neurogastroenterology reflect this treatment order [6, 7].

So, to recap, antimicrobial agents feature as the third step in the following treatment pathway:

  1. Reset: Make dietary changes that will help reset your gut health and serve as the foundation to your future health.
  2. Support: Add effective probiotics that will support your gut health with helpful bacteria.
  3. Remove: If symptoms persist, antimicrobials can remove remaining pathogens that could be continuing to harm your health.

Let’s look at these in turn:

Reset Your Gut Through Diet

A diet that eliminates potentially inflammatory foods and foods that could stimulate an immune reaction can be hugely beneficial to your overall health and is always the first place to start.

I recommend beginning with a Paleo-style diet, which is low in potentially inflammatory foods including dairy and gluten, but rich in plenty of nutrient-rich fruit and vegetables.

For many people, this will be enough to allow the gut to start to reset and heal.

However you can move to a slightly stricter low FODMAP diet if you don’t get a satisfactory level of symptom improvement. The low FODMAP diet helps to reduce bacterial overgrowth by restricting foods that feed bacteria. It has been shown to be very helpful for gut issues in particular, especially IBS [8, 9, 10, 11].

Can an Elemental Diet Help?

More recently, many of my patients have found an elemental formula hugely effective either alone or in association with a Paleo or FODMAP diet. You don’t have to replace every meal if you don’t want to, and just replacing breakfast and/or lunch is enough to help the gut rest and repair for some people.

What’s more, research has shown that elemental diets can significantly improve symptoms for those with IBD, IBS, SIBO, and other digestive disorders [12, 13, 14, 15, 16, 17, 18]. 

Probiotic Supplements 

Probiotics are the next step after diet and can create powerful improvements in your gut and microbiota health.

  • For example, a meta-analysis of 18 studies found that probiotics significantly improved bacterial overgrowth and helped reduce abdominal pain for SIBO patients [19].  
  • One SIBO-probiotics study found probiotics to be more effective than Metronidazole, an antibiotic treatment for SIBO [20].
  • Multi-strain probiotics also help improve abdominal pain and discomfort for those with IBS [21].
  • S. boulardii (a healthy fungus) has been shown effective in treating digestive tract parasites such as amoebas, giardia, and Blastocystis hominis [22].
  • In general, probiotics help to reduce inflammation, fight intestinal pathogens and toxins, and improve the bacterial composition of the gut, which can help to generally support digestive function and overall human health [19, 23, 24]. 

Research suggests the best results can be obtained by including a diversity of high-quality probiotics. For example, two systematic reviews and meta-analyses indicated that multi-strain probiotics were more effective than single-strain probiotics for treating IBS [25].

Most probiotics fall into one of these three categories. For best results, I suggest you take one probiotic from each category:

Antimicrobial Agents

The time to introduce antimicrobial agents is if some stubborn symptoms remain after you’ve reset your diet and supported your system with probiotics for a couple of weeks. This whole process may take anywhere from a few weeks to a few months depending on how much experimentation is needed to identify your ideal diet.

As I write in Healthy Gut, Healthy You, rather than trying to pinpoint exactly what “bad” microbe might be causing you problems, a holistic approach with medicinal plants that have broad spectrum antimicrobial approaches is often most helpful.

Some medicinal plants and herbs have demonstrated antibacterial, antifungal, antiviral, and antiparasitic capabilities and are valuable for controlling infectious microbes [26].  

Antibacterials can be “cidal” (as in bacteriocidal, meaning they actually kill bacteria) or “static” (as in bacteriostatic, meaning they stunt or have a regulatory effect on bacteria growth).

The way antibacterials target harmful bacteria is three-fold [1]:

  1. They can break down the bacterial cell wall
  2. They can target bacterial ribosomes (part of the genetic material inside bacteria)
  3. They can destroy bacterial enzymes involved in bacterial reproduction

Benefits of Antimicrobials 

The benefits of antimicrobials are broader than just killing harmful microorganisms. Other beneficial effects extend to mental health and general well being. 

Here are some examples of antimicrobial agent benefits supported by research:  

  • Improved cognitive function: A recent systematic review found that berberine may inhibit the development of dementia by preventing brain damage and enhancing cognition [27].
  • SIBO treatment: In one study, a mixture of herbal antimicrobial agents that included berberine and oregano oil was as effective at taming small intestinal bacterial overgrowth as the antibiotic Rifaximin [28].
  • Reduced mental fatigue: Taking peppermint oil capsules improved performance and reduced fatigue in people given a cognitively demanding task [29].
  • Inflammation relief: A high-quality 2019 review found that berberine appears to decrease serum C-reactive protein levels in the blood — indicating a reduction in chronic inflammation [30].

Some Effective Antimicrobial Agents

Most herbal anti-bacterial, antiviral and antifungal agents have been studied in laboratory and animal studies but not yet in human clinical trials. 

We do, however, have excellent evidence that conventional pharmaceutical antibiotics can offer benefits for conditions such as SIBO. We can infer from these studies that natural, plant-based equivalents could also curb harmful bacteria overgrowths (and may be kinder on the system).

Here are some interesting antimicrobials and the research behind them:


Active IngredientsAntimicrobial EffectOther BenefitsSources
Thymol and carvacrol (in oregano oil)Antibacterial, antiviral, antifungal, antioxidant, insecticidal Pain-relieving and liver-protective effects have been noted. May act as an antidepressant. Antibacterial effects against harmful bacillus species have also been reported.[31, 32, 33]


Active IngredientsAntimicrobial EffectOther BenefitsSources
Berberine, which naturally occurs in various plants, including Oregon grape and goldensealEffective antimicrobial agent and anti -inflammatory May inhibit dementia by preventing brain damage. Beneficial effect on high blood cholesterol and triglycerides. Improved diarrhea symptoms in IBS; may also help H. pylori eradication and reduce colorectal adenoma recurrence. [27, 34, 35, 36, 37, 38]

Sweet Wormwood (Artemisia Annua)

Active IngredientsAntimicrobial Effect Other BenefitsSources
ArtemisininAntimicrobial, antiparasitic,antifungal and anti-inflammatory; has gut microbiome modulating effects. An FDA-approved derivative of artemisinin achieved faster parasite clearance combined with a sulfonamide (antibiotic also known as “sulfa drug”) than sulfonamide alone. Has antimalarial effects.[39, 40, 41, 42, 43]

Peppermint Oil

Active IngredientsAntimicrobial EffectOther BenefitsSources
Various: Includes limonene, cineole, menthone, menthol, pulegone, and carvone Antifungal, antimicrobial, and antiparasitic propertiesVery effective in easing pain and bloating in IBS. Boosts alertness. Peppermint oil inhalation had an antibacterial effect alongside multidrug therapy in tuberculosis. [29, 44, 45, 46, 47]

Caprylic Acid

Active IngredientsAntimicrobial EffectOther BenefitsSources
Caprylic acid: a fatty acid that occurs in large quantities in coconut oilAntibacterial, antifungalMay have neuroprotective effects. May benefit chronic upper respiratory tract infection, tooth infection, and cytomegalovirus infection.[48, 49]

Natural vs Pharmaceutical Antimicrobials

Medicine and herbs on a wooden surface and a stethoscope on a white surface

In a few cases, targeted use of conventional antibiotics or antimicrobial drugs may be warranted for specific bacterial infections or other infectious diseases. For example:

  • Rifaximin or Rifaximin with neomycin for SIBO [50, 51]
  • Fluconazole as an inhibitor of fungal infections
  • Flagyl to help eradicate protozoa.

While these pharmaceuticals can be very helpful in certain cases, they don’t tend to have the broad spectrum disinfectant action plant versions do — just one herb can kill bacteria, fungi, and protozoa [26].

Nevertheless, they do have their place. Discuss the pros and cons of conventional versus more natural options with your doctor.

Potential Antimicrobial Side Effects

As antimicrobial agents can be powerful, they need to be treated with respect. You should be aware that they can come with potential side effects.

Die-off Effect

One of these potential side effects occurs when bad bacteria die inside your body, causing what’s known as a die-off reaction. It may lead to:

  • Increased fatigue
  • Headaches
  • Digestive upset
  • Flu-like symptoms

Fortunately, a die-off reaction should last no more than a few days to a week. It’s also a good sign that your antimicrobial regimen is working.

If, however, your reaction doesn’t go away after a week, you may be allergic to something in the antimicrobial formula you are taking. In this case, my advice would be to stop taking all antimicrobials for a few days and see how you feel. 

You could then introduce individual antimicrobials one at a time to isolate what you had a problem with. Or, the antimicrobial may be effective, but you may need a lower dose. Consult with your doctor about why your reaction symptoms aren’t going away.

Resistant Bacteria

Antimicrobial resistance is the process of bacteria, viruses, fungi, or parasites changing over time so their susceptibility to antimicrobials decreases. This is a threat to public health, as it increases the difficulty of treating infections and raises the risk of disease spread and serious illness [52].

Intrinsic antibiotic resistance is when a microorganism has a natural feature protecting it from being destroyed by an antimicrobial agent. An example of intrinsic resistance can be found in “gram-negative bacteria” — resistant strains that have developed an outer membrane around their thin bacterial cell wall, protecting them from some types of antibiotics.

Acquired resistance is more serious. It occurs when a bacterium (gram-positive type in this case) that was once susceptible to antimicrobials develops resistance over time. An example is in methicillin-resistant Staphylococcus aureus, or MRSA. 

The worst case scenario is when there are no new drugs left to treat disease-causing bacteria. For example, vancomycin is the antibiotic of last resort in Western medicine, yet a few bacteria have already started to become resistant to it [1].

  • The bad news: Resistance to antimicrobials is almost inevitable because of the prevalence and huge diversity of microorganisms. 
  • The good news: Functional and herbal medicine can help, as herbal compounds have a broad-acting pharmacology, enabling control of pharmaceutical-resistant organisms [53]. 

The Bottom Line

Antimicrobial agents help people to resolve stubborn health problems that originate from microbial imbalances in the gut. They should generally come into play only after you have first changed your diet and taken a course of multi-strain probiotics.

Choosing the right antimicrobial and navigating your way through potential side effects isn’t always easy on your own. Consider scheduling a virtual or in-person consultation at our functional medicine center, or check out my book, Healthy Gut, Healthy You, for more guidance.

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