Antimicrobials vs. Antibacterials for Brain Fog, Gut Issues, and More

Antimicrobial vs. Antibacterial Use for IBS, Infection, and Brain Fog.

Antibacterials and antimicrobials can be key for healing chronic health issues such as irritable bowel disease (IBD,) small intestinal bacterial overgrowth (SIBO,) or H. pylori infections. However, the terms aren’t interchangeable. This article will help you know what antimicrobials and antibacterials are, the differences between antimicrobials vs. antibacterials, how they can treat health conditions, when to use them, and how they are used in functional medicine.

Antimicrobial vs antibacterial: Woman with a headache lying on the couch

The Difference Between Antimicrobials vs. Antibacterials

Antimicrobials and antibacterials are used in everything from hand soap and hand sanitizer to prescription antibiotics. However commonplace they are, many people don’t understand the differences between antimicrobials vs. antibacterials.

The best way to remember the difference between antimicrobials and antibacterials is that antibacterials are antimicrobials, but not all antimicrobials are antibacterials.

An antimicrobial is anything that kills or prevents the growth of a living organism. [1] There are four types of antimicrobials, and each target a different kind of microorganism [1]: 

  • Antibiotics (antibacterials): used for bacteria 
  • Antivirals: target viruses 
  • Antifungals: target funguses 
  • Antiprotozoals: target parasites (protozoa)

The term “antibacterial” is commonly used to mean anything that kills off a bacteria or virus. For example, many people refer to Lysol spray as an antibacterial spray, but it is really an antimicrobial product because it will kill bacteria and viruses. It is also helpful to remember that many antimicrobials kill multiple types of pathogens. For example, a common antibiotic, Flagyl, targets bacteria and parasites.

Antimicrobial vs antibacterial: Diagram of various bacteria and viruses with prohibition signs

Common Types and Uses of Antimicrobials and Antibacterials

Let’s look at some different types of antimicrobials and what they are used for:

  • Antiseptics: used on living organisms (like the skin) to kill various microbes such as bacteria and viruses. Hydrogen peroxide is an antiseptic, and antibacterial soaps are over-the-counter antiseptics that have active ingredients that inhibit bacterial growth. 
  • Disinfectants: used on non-living surfaces (like countertops and medical supplies) to kill mildew or microbes that may cause infection. Cleaning products like this are technically classified by the environmental protection agency as pesticides, which just means that they have antimicrobial properties and can stop the growth of bacteria.  
  • Antibiotics: antibiotic agents used to kill bacteria — can be herbal or lab created, such as berberine or penicillin
  • Antifungals: used to kill or inhibit overgrowth of fungi, such as oil of oregano, which can be used for yeast (candida) and tinea (which causes Athlete’s foot)
  • Antiprotozoals: treat parasites but are called by the issue they treat (ex., antimalarial drugs) rather than “antiprotozoals.”

Since antimicrobials cover such a wide variety of microorganisms, this chart outlines some of the common issues antimicrobials may be used for and what types of microorganisms they are:

Bacteria VirusesFungiProtozoa/Parasites
SIBO (small intestinal bacterial overgrowth)

H. pylori infection (often found in gastritis)

Staphylococcus aureus (staph infection)

Escherichia coli (E.coli)

Salmonella

Halitosis (bad breath)
Chickenpox and shingles

Herpes virus

RSV (respiratory syncytial virus)

Coronavirus

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

Tapeworm

Roundworm
Antimicrobial vs antibacterial: Yellow capsules

How Herbal Antimicrobials Work

Herbal antimicrobials can be used to treat gut infections (small intestinal bacterial overgrowth (SIBO) SIFO (small intestinal fungal overgrowth), and H. pylori) and the stomach distress and fatigue that come with them. They can also be used as part of a treatment plan for IBD’s such as ulcerative colitis and Crohn’s disease (more on this later). Herbal antimicrobials are often just as effective as lab created antimicrobials but they typically have far fewer side effects. [2 Trusted SourcePubMedGo to source, 3]

When many types of plants break down (metabolize) they create either a barrier to microbes or induce antimicrobial agents. Because of these antimicrobial properties, we can use them to treat bacterial infections or overgrowth of bacteria, viruses, and fungi in humans. [4 Trusted SourcePubMedGo to source]

Herbal Antimicrobials as Treatment Options

Herbal antimicrobials are often a better choice for treatment because they:

Let’s look at some of the research behind a few herbal antimicrobials and the conditions they can help treat:

ConditionHerbal Antimicrobials UsedSupporting Research
IBS (irritable bowel syndrome)Oil of oregano

Zataria multiflora

Peppermint oil
The compounds thymol and carvacrol in oregano and zataria multiflora improved symptoms, some had up to a 75% reduction. [9 Trusted SourcePubMedGo to source]

Peppermint oil has been widely tested and shown to improve motility, reduce inflammation, and improve gut microbiota. [10 Trusted SourcePubMedGo to source, 11 Trusted SourcePubMedGo to source, 12 Trusted SourcePubMedGo to source, 13 Trusted SourcePubMedGo to source]
IBD: Ulcerative colitis and Crohn’s diseaseArtemisia absinthium (wormwood, but not sweet wormwood)

Curcumin (turmeric)
In colitis and Crohn’s, Artemisia absinthium induced clinical remission. [14 Trusted SourcePubMedGo to source, 15 Trusted SourcePubMedGo to source, 16 Trusted SourcePubMedGo to source]

Curcumin is anti-inflammatory and helps maintain remission of colitis. [17 Trusted SourcePubMedGo to source]
H. pylori infectionBerberineAdding antimicrobial therapy for H. pylori improves the eradication rate, peptic ulcer healing, and reduced side effects, compared to regular therapy without berberine. [5 Trusted SourcePubMedGo to source]
Mood and cognitive declineBerberine

Peppermint oil
Berberine may prevent brain damage associated with dementia by reducing metabolic dysfunction. [8 Trusted SourcePubMedGo to source] It has also been shown to reduce depression rates. [7 Trusted SourcePubMedGo to source]

Peppermint oil has been shown to improve the ability to complete cognitive tasks. [18 Trusted SourcePubMedGo to source]
SIBOBerberine

Pau d’arco (Quercetin)
Herbals used together have been found to be as effective as traditional antibiotics at treating SIBO, and may be particularly helpful in cases where traditional antibiotics have not worked. [19 Trusted SourcePubMedGo to source, 20 Trusted SourcePubMedGo to source]
Insulin resistanceShirazi thyme (Zataria multiflora)A randomized control trial showed that thyme decreased blood insulin levels and improved insulin resistance. [21 Trusted SourcePubMedGo to source]

Essential Steps Before Using Antimicrobials 

Antimicrobial vs antibacterial: 3 steps for gut health

In order to find the least invasive treatment with the least side effects, it’s best to start with resolving gut bacteria imbalances and infections with diet and probiotics. Antimicrobials can be used later if needed.

You can find these three steps in my book, Healthy Gut, Healthy You:

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

Let’s take a closer look at each of these steps:

Reset: Anti-Inflammatory, Gut Supportive Diet

An anti-inflammatory diet that removes foods that may cause an immune reaction is the first place to start. Not only may this help reduce symptoms, but the diet may help rebalance the microbiome. 

I recommend starting with a Paleo diet, which removes inflammatory foods such as gluten, dairy, and legumes. However, a more restrictive diet may be needed if you do not see enough gut health improvement. 

Research shows that  an anti-inflammatory diet can:

Support: Probiotics to Support the Gut Microbiome

Probiotics can help support your gut reset by balancing out the gut microbiome and should be used at the same time as your gut reset: 

Here is a simple chart outlining how to add probiotics into your life:

Antimicrobial vs antibacterial: Probiotic easy protocol

Probiotic triple-therapy involves using three different classes of probiotic: a blend of lactobacillus and bifidobacterium, saccharomyces boulardii, and soil-based. [34] Meta-analyses show that taking multiple strains of probiotics are more effective than taking a single-strain probiotic. [35 Trusted SourcePubMedGo to source, 36 Trusted SourcePubMedGo to source

In order to have the most success with the support step choose one probiotic from each category above in order to get multiple strains. 

If these first two steps of reset and support do not resolve symptoms enough, you can move on to the “remove” step. In this step, you can use probiotics along with antimicrobials, which has been shown to be especially beneficial. For example: 

Remove: Using Antimicrobials to Get Rid of Bad Microbes

If the first two steps do not resolve symptoms, it’s often time to move on to removing any unwanted gut bacteria, fungi, or parasites with antimicrobial herbs

You may be wondering if testing is needed to know exactly which antimicrobials to take. Herbal antimicrobials are often broad-spectrum, meaning they fight off a few different microbes at once. Using broad spectrum herbal antimicrobials can allow us to resolve the offending microbes, without needing extensive and expensive testing. 

Herbal antimicrobials may also help to resolve other chronic health issues, such as IBS, cognitive decline, brain fog, fatigue, and high cholesterol. [8 Trusted SourcePubMedGo to source, 40 Trusted SourcePubMedGo to source, 41 Trusted SourcePubMedGo to source] Antimicrobials may be used in these cases because many of these illnesses have a contributing root cause of a pathogenic infection and/or inflammation. [42 Trusted SourcePubMedGo to source]

You may be used to antibiotics being given over 3-10 days, on average. Herbal antimicrobials are given over a longer period of time, often a few months, until you consistently feel better. If after a few months off of the antimicrobials, symptoms come back, another round may be necessary. 

Antibiotic Resistance: Are Antibacterials Bad for You? 

Overuse of antibiotics (one form of antibacterial) can lead to illness later in life. In fact, one systematic review found the risk of irritable bowel disease (IBD) increased in people who used antibiotics as a child, especially when children were raised in the U.S., where antibiotics are used more often early on in life. [43 Trusted SourcePubMedGo to source, 44 Trusted SourcePubMedGo to source]

Overuse of antibiotics in healthcare has also led to antibacterial resistance, which is when the microbes (bacteria, viruses, fungi, or parasites) mutate over time or acquire resistance genes, so antimicrobials no longer work against them. [1] This is especially harmful when a microbe becomes resistant to broad-spectrum antibiotics, like in the case of MRSA (Methicillin-resistant Staphylococcus aureus). MRSA is a risk in healthcare facilities where antibiotics are used regularly.

While there are risks, antibiotics have also changed quality of life and greatly reduced mortality from infectious diseases around the world when used correctly. 

Fortunately, herbal antimicrobials have demonstrated antibacterial, antifungal, antiviral, antiparasitic, and anti-biofilm properties. They are also anti-inflammatory and preliminary research suggests they may have antidepressant properties. [14 Trusted SourcePubMedGo to source, 45 Trusted SourcePubMedGo to source] They have fewer side effects than lab-created antibiotics, and they have the diversity to help kill pathogens that have developed drug antibiotic resistance. [2 Trusted SourcePubMedGo to source, 3]  

Benefits of herbal antimicrobials

Simplifying Your Treatment

If you are experiencing chronic health issues, as mentioned above, and have not found relief, the simplest course of action is:

  • Reset the gut with an antiinflammatory diet
  • Support the gut with probiotics

If those two steps still do not resolve symptoms, then we can use a broad spectrum mix of herbal antimicrobials. This can be done safely even if we do not know exactly which microbes may be causing symptoms.

I hope this article has helped clear up the confusion of antimicrobials vs. antibacterials and shown you how beneficial antimicrobials can be when used as part of a measured treatment plan. If you need more help figuring out a more personalized treatment plan, apply to become a patient at our clinic.

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