Antimicrobials vs. Antibacterials: What’s the Difference?

Antimicrobial vs antibacterial: essential oil dripping from a leaf into a bottle

There’s a lot of talk around antibacterial and antimicrobial products — everything from soaps to supplements. Though many of these products are labelled interchangeably, there are key differences between antibacterial and antimicrobial agents, especially in functional medicine. What are the differences between the two, and when should you use each of them on your healing journey? 

In this article, we will review the properties of antimicrobials vs antibacterials, how they are used from cleaning surfaces to treating infections, the benefits and drawbacks of each, and more. 

We’ll also discuss the use of herbal antimicrobials for specific conditions, from IBS and SIBO to insulin resistance and cognitive decline.

The Difference Between Antimicrobials vs. Antibacterials

Here’s the main difference between antimicrobials and antibacterial agents: All antibacterials are antimicrobials, but all antimicrobials are not necessarily antibacterials. 

An antimicrobial refers to any agent that kills or prevents the growth of any living organism, including [1]:

  • Antibiotics or antibacterials: used to kill bacteria, such as E. coli or H. Pylori
  • Antifungals: used to kill fungi, such as candida
  • Antiprotozoals: used to kill parasites (protozoa), such as Lyme or tapeworm
  • Antivirals: target viruses, such as herpes or influenza

By definition, an antibacterial technically only kills bacteria. However, the term “antibacterial” is commonly used to describe something that kills both bacteria and viruses. Lysol spray is a common example. It is marketed as an “antibacterial” spray, but it is really antimicrobial since it kills both bacteria and viruses when sprayed on non-organic surfaces.

Even some pharmaceutical antibiotics kill multiple types of pathogens, despite being labelled as an antibiotic/antibacterial. The common antibiotic Flagyl is one example. It kills both bacteria and parasites. 

Common Antimicrobial and Antibacterial Types and Uses

Antimicrobial vs antibacterial: person wiping a kitchen counter

There are several different types of antimicrobials from cleaning products to herbal formulas to pharmaceuticals. Let’s look at what these types are and how they are used: 

  • Disinfectants: These are used on inorganic surfaces (non-living) such as countertops to kill potentially harmful microbes, like bacteria and viruses, and prevent growth of microorganisms. These antibacterial products are classified as pesticides by the environmental protection agency, which means that they are known to kill bacteria and other microbes. 
  • Antiseptics: These are similar to disinfectants, but they can be used on organic surfaces, like skin or even orally. They are also antimicrobial, capable of killing a wide spectrum of pathogens. Hydrogen peroxide, antibacterial soap, and hand sanitizer are examples of antiseptic solutions. 
  • Antibiotics: Antibiotics are used to kill bacteria, but they can be pharmaceutical or herbal. Berberine is an herbal antibiotic, while penicillin is a pharmaceutical antibiotic. 
  • Antiprotozoals: These are parasite-killing drugs, but they are referred to by what parasite they treat. For example, see antimalarial drugs. You may also hear “antiparasitic” used in place of antiprotozoal. 
  • Antifungals: Antifungals kill or inhibit fungal growth, just as their name would suggest. Oil of oregano is one example of an herbal antifungal often used to fight candida and tinea or Athlete’s foot. 

This chart outlines some of the microorganisms these antimicrobial agents may be used for. 

Bacteria VirusesFungiProtozoa/Parasites
SIBO (small intestinal bacterial overgrowth)
H. pylori infection (often found in gastritis)
Staphylococcus aureus (staph infection)
Escherichia coli (E.coli)
Halitosis (bad breath)
Chickenpox and shingles
Herpes virus
RSV (respiratory syncytial virus)
Influenza (flu)
SIFO (small intestinal fungal overgrowth)
Candida (yeast) overgrowth
Athlete’s foot
Jock itch
Tinea versicolor (fungal infection of the skin)
Giardia infection
Malaria (caused by Plasmodium)
Lyme disease

Are Antibacterials Bad for You? (Antibiotic Resistance)

Overuse of antibiotics has become a significant issue. For example, research shows that people who use antibiotics early in life and often, which is common in the U.S., are more likely to develop irritable bowel disease (IBD) [2, 3]. 

In healthcare at large, an overuse of antibiotics has led to antibacterial resistance, which occurs when microbes mutate, evolve, and become insusceptible to antibiotic treatment. MRSA (methicillin-resistant Staphylococcus aureus) is one example of a microbe that became resistant to broad-spectrum antibiotics and is now a great risk for patients in healthcare facilities where antibiotics are often used. 

However, antibiotic treatment has also saved countless lives and continues to reduce mortality from life-threatening diseases around the world. 

But we can also turn to herbal antimicrobials for fighting infections, including bacterial, parasitic, fungal, and viral illnesses. Herbal antimicrobials also have anti-biofilm, anti-inflammatory, and even antidepressant characteristics [4, 5]. They have fewer side effects than pharmaceutical antibiotics, and they have the diversity to help kill pathogens that have developed drug antibiotic resistance [6, 7].

Antimicrobial vs antibacterial: Herbal Antimicrobials Benefits infographic by Dr. Ruscio

Herbal Antimicrobials

Herbal antimicrobials have many uses, including treating gut infections like SIBO (small intestinal bacterial overgrowth), SIFO (small intestinal fungal overgrowth), H. Pylori, candida, and others. By addressing these infections, herbal antimicrobials can help relieve symptoms like fatigue, brain fog, and gastrointestinal distress. 

They can also be used to treat inflammatory bowel disease, Crohn’s disease and ulcerative colitis. Herbal antimicrobials are often just as effective as pharmaceutical interventions, and they typically have fewer side effects [6, 7].

These herbal agents contain antimicrobial properties for their own protection. When we eat and digest them, these metabolites are released and they go to work fighting against certain pathogens [8].

Benefits of Herbal Antimicrobial Therapy

When you’re dealing with an infection, especially one in the gut, it can sometimes be difficult to address. You might be dealing with more than one kind of pathogen, and treatment with antibiotic or antifungal medications may not be enough. In these cases, herbal antimicrobials are beneficial in several ways: 

  • They tend to have fewer side effects than pharmaceutical medications [9].
  • They often work on a more broad-spectrum level, helping to get rid of various kinds of bacterial infections, fungi, parasites, and other pathogenic microbes.
  • They help reduce antibacterial resistance and break biofilms [6].
  • They may also contribute other positive effects, like improving cognitive function, and decreasing fatigue and depression [10, 11, 12].

Let’s review some of the research behind a few herbal antimicrobials and the conditions they can help treat.

Antimicrobial vs antibacterial: fresh herbs on a wooden plate

IBS (Irritable Bowel Syndrome)

Herbal antimicrobials that may help: Oil of oregano, zataria multiflora, peppermint oil.

There are two beneficial compounds, thymol and carvacrol, that are found in oil of oregano and zataria multiflora. Research has shown that these compounds can improve IBS symptoms by as much as 75% in some cases [13].

Peppermint oil has also been shown to improve gut health, including by enhancing motility, improving microbiome balance, and reducing inflammation [14, 15, 16, 17].

IBD, Ulcerative Colitis and Crohn’s Disease

Herbal antimicrobials that may help: Artemisia absinthium (wormwood, but not sweet wormwood), curcumin (turmeric).

Several studies have shown that Artemisia absinthium can induce clinical remission in IBD patients [4, 18, 19].

Curcumin, the active component of turmeric, is an anti-inflammatory compound that helps maintain remission of ulcerative colitis [20].

H. Pylori 

Herbal antimicrobials that may help: Berberine

Berberine is an effective addition to conventional H. Pylori treatment, improving eradication rate and ulcer healing as well as reducing side effects [9].

Mood and Cognitive Decline

Herbal antimicrobials that may help: Berberine, peppermint oil

Berberine has been shown to prevent metabolic dysfunction, which may help prevent brain damage associated with dementia [12]. It has also been shown to reduce depression rates [11].

Peppermint oil has also been shown to improve cognitive ability in completing certain tasks, like rapid visual information processing [21].


Herbal antimicrobials that may help: Berberine, Pau d’Arco, quercetin

Herbal formulas using berberine and pau d’arco have been found to be as effective as traditional antibiotics for treating SIBO, and may even help in cases where antibiotics were ineffective [22, 23].

Insulin Resistance

Herbal antimicrobials that may help: Shirazi thyme (Zataria multiflora)

A randomized control trial showed that thyme decreased blood insulin levels and improved insulin resistance [24].

Antimicrobial vs antibacterial: 3 Steps for Gut Health infographic by Dr. Ruscio

Before You Use Antimicrobials

Using antimicrobials without a strong foundation of diet and probiotics in place is like cutting out weeds from your garden without taking out the whole root. Your garden might look weed-free for a while, but soon enough, they will grow back. 

The most sustainable way to improve your gut health is to find the right diet that gives you the nutrients your body needs to heal, supporting your microbiome with probiotics that will begin to address any infections present, and finally adding in antimicrobials if needed. 

I outline this process in my book, Healthy Gut, Healthy You

  • Reset your gut by changing your diet and lifestyle
  • Support the gut with probiotics 
  • Remove any unwanted gut bacteria, fungi or parasites with antimicrobial herbs

Here’s a closer look at this process:

Reset Your Diet

An anti-inflammatory diet can set the stage for gut healing by removing foods that may cause an immune reaction. Plus, an anti-inflammatory diet is key for helping to rebalance the microbiome. 

The Paleo diet is often the best place to start, since it removes inflammatory grains, dairy, and legumes, which many people find challenging to digest. But there are other diets you can try if you don’t see enough improvement on Paleo.

Research shows that an anti-inflammatory diet can:

  • Lower inflammation in the gut, which can help regulate gut bacteria [25, 26]
  • Improve IBD symptoms [27, 28]
  • Reduce foods that aggravate SIBO [29] (Combined with probiotics, this can be a powerful SIBO treatment [30]

Support With Probiotics

Along with changing your diet, probiotics can help reset your gut by adding beneficial strains of bacteria to your microbiome.

  • When comparing probiotics to the antibiotic metronidazole for the treatment of SIBO, one study found probiotics to be more successful [31].
  • Probiotics also reduce inflammation and support a healthy immune response in the gut [32, 33, 34, 35].
  • Some research shows that probiotics may help prevent or treat viruses and colds, including upper respiratory tract infections [36].

The graphic below shows how you can add probiotics into your life and monitor your response. Probiotic triple therapy, using one probiotic from each of the three main categories, has been key for many positive patient outcomes we’ve seen in our clinic. 

With probiotic triple therapy, you combine a multistrain blend of lactobacillus and bifidobacterium, a saccharomyces boulardii probiotic, and a soil-based probiotic. Meta-analyses show that taking multiple probiotic strains has a greater effect on the microbiome than taking only a single-strain probiotic [37, 38].

Probiotic Easy Protocol infographic by Dr. Ruscio

If these first two steps are not enough to resolve your gut issues, you can move on to the remove step, where you will combine probiotics with antimicrobials.

Combining probiotics and antimicrobials has been shown to have significant benefits:

  • Probiotics and antibiotics used together improved the treatment of SIBO [31, 39], even doubling the effectiveness in one study [40].
  • When treating H. Pylori infection, patients taking probiotics and antibiotics together saw better results than with antibiotics alone [41].

Remove Bad Microbes with Antimicrobials

Antimicrobial herbs come into play when symptoms do not resolve with diet and probiotic therapy alone. 

Fortunately, many antimicrobial herbs work on a broad-spectrum basis, meaning they kill multiple types of pathogens at once. This allows you to resolve microbial infections without requiring expensive and unnecessary testing to identify the exact microbe(s) present. 

Herbal antimicrobials may also help resolve other chronic issues, like brain fog, cognitive impairment, IBS, high cholesterol, and fatigue [12, 42, 43]. Antimicrobials can be helpful for these conditions because there is often a pathogen component at the root of these symptoms, along with inflammation [44].

While antibiotics are prescribed for a period of 3-10 days on average, antimicrobials often take a few months to reach their highest level of efficacy. Sometimes, you need to alternate or rotate different antimicrobial agents to completely address the pathogen(s). Or, if symptoms return once antimicrobials are stopped, you may need another round.

Woman enjoying the scent of a fresh cup of coffee

Healing Step by Step

Antimicrobials (including antibacterials) are just one part of the gut healing process. You should always start with changing your diet and lifestyle and taking probiotics. If those two things don’t resolve your symptoms, you can consider adding antimicrobial herbs as a next step. 

It’s important to follow this protocol to: 

  1. Build a foundation for gut health that lasts beyond the treatment period
  2. Know what therapies work for you and what could still be improved. 

If you need guidance and support to address your symptoms, reach out to us at the Ruscio Institute for Functional Medicine and become a patient today.


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