Dr. Michael Ruscio, DC is a clinician, Naturopathic Practitioner, clinical researcher, author, and adjunct professor at the University of Bridgeport. His work has been published in peer-reviewed medical journals and he speaks at conferences around the globe.
How to Get Rid of Unhelpful Microorganisms and Improve Your Gut Health
Antimicrobials and antibiotics both help to get rid of unwanted microorganisms.
Antibiotics target bacteria, while antimicrobials may also knock out other microbes and pathogens, for example, fungi and parasites.
Long-term imbalances in the gut microbiota (microflora) can respond to either an antibiotic or an antimicrobial, depending on the specific condition.
Another way of thinking of antimicrobial vs. antibiotic is in terms of “natural” (herbal antimicrobial agents) vs. “pharmaceutical” (conventional antibiotic drugs).
On the whole, herbal antimicrobials are preferred for many (but not all) gut issues.
However, you should sort out your diet and take probiotics first, only introducing herbal antimicrobials later, if still needed.
Antimicrobial vs. antibiotic — while these terms are sometimes used interchangeably there’s a difference between the two, which can have implications for healing poor gut health.
For example, H. pylori infections, which can cause stomach ulcers, are caused by just one specific bacteria and can be treated by one specific antibiotic.
On the other hand, generalized gut dysbiosis may be caused by imbalances in many types of microorganisms (not just bacteria). In this case, a broad-spectrum antimicrobial agent may be a better treatment.
Antimicrobial vs. Antibiotic: A Simple Distinction
To hone in on the antimicrobial vs. antibiotic distinction more directly:
An antimicrobial is anything that kills or prevents the growth of a living microorganism (microbe) .
An antibiotic is a specific type of antimicrobial, used for fighting bacterial infections. It either kills bacteria (bactericidal) or inhibits them (bacteriostatic).
An antibiotic is always an antimicrobial, but an antimicrobial isn’t always an antibiotic.
Types of Antimicrobials
Broadly speaking, there are four main types of antimicrobials, each killing or inhibiting the growth of a different kind of microorganism :
Antibiotics, such as penicillin (antibacterials), kill bacteria such as staphylococcus aureus, E. coli, and so on
Antivirals target viruses
Antifungals target fungi and yeasts
Antiprotozoals target parasites (protozoa)
Some antimicrobials can have broad-spectrum actions. For example, just one herb can kill a range of bacteria, fungi, and protozoa .
Sanitizers and disinfectants are other names given to antimicrobials that kill a range of microbes, in this case usually on physical contact (for example when sprayed onto kitchen surfaces).
Pharmaceutical or Herbal Antimicrobials?
Distinguishing antimicrobial vs. antibiotic isn’t the only thing to think about. You’ll also need to consider if a pharmaceutical or more natural approach is better for you.
Functional medicine practitioners don’t generally like using conventional antibiotic drugs because they tend to be more aggressive in their effects and have a higher potential to cause antibacterial or antibiotic resistance.
I take the view that as long as they’re not overused, pharmaceuticals may sometimes be the right option for specific bacterial infections, overgrowths, or infectious diseases. For example, these can be legitimate uses of antibiotics:
Rifaximin or rifaximin with neomycin for SIBO (small intestinal bacterial overgrowth) [3, 4]
Fluconazole as an inhibitor of fungal infections 
Pharmaceuticals can be very effective. However, if you can achieve good relief with herbal antimicrobials this is usually better because :
Herbs have a broad-acting pharmacology, enabling control of drug-resistant bacteria.
Herbs don’t tend to contribute to the public health problem of resistant bacteria in the same way as conventional drugs. (Antimicrobial resistance occurs when bacteria develop mutations that mean they can escape being knocked out by antimicrobial drugs.)
Herbal antimicrobials haven’t been thoroughly tested in too many human diseases yet. However, below are details of four gut health conditions where the research is already quite convincing.
Irritable bowel syndrome (IBS)
Thymol and carvacrol (found in oregano oil and zataria multiflora)
Thymol and carvacrol improved IBS symptoms such as pain and inflammation, in some cases by as much as 75% .
Peppermint oil has been widely tested in IBS and shown to improve motility, reduce inflammation, and improve gut microbiota [9, 10, 11].
H. pylori infection
Adding berberine to conventional therapy for H. pylori improved the eradication rate, peptic ulcer healing, and reduced side effects .
SIBO (small intestinal bacterial overgrowth)
Berberin, oregano, artemisia, pau d’arco
A combination of these herbs, and others, was at least as effective as rifaximin in people with SIBO . Herbal antimicrobials also produced fewer side effects.
Inflammatory bowel disease
In colitis and Crohn’s, Artemisia absinthium induced clinical remission [10, 11, 14]. Anti-inflammatory curcumin helped maintain remission of colitis .
Other Benefits of Herbal Antimicrobials
Another advantage to using plant-based antimicrobials is that they may have extra positive effects, beyond killing harmful microorganisms in the gut.
Here are some wider benefits of antimicrobial agent benefits, supported by research:
Improved cognitive function: A systematic review found that berberine may help inhibit the development of dementia by preventing brain damage and enhancing cognition .
Better mental stamina: Consuming peppermint oil helped people perform better and tire less quickly when given a mentally demanding task .
Decreased inflammation: A high-quality research review found that supplementing with berberine was correlated with a reduction in a marker of inflammation (C-reactive protein) in the blood — indicating a reduction in chronic inflammation .
How and When to Introduce Antimicrobials
Let’s imagine you have troublesome gut-related symptoms, which can vary from bloating, IBS, Crohn’s, and colitis, to food sensitivities, fatigue, and brain fog.
Given some of the evidence you’ve read above, herbal antimicrobials may sound like the treatment you’d want to opt for right away. However, I actually don’t recommend them as a first step for alleviating chronic gut health issues.
Instead, the science points to sorting out your diet as a first priority, with probiotics as a secondary step. Antimicrobials are a treatment option to consider only after these two foundational steps.
Globally, good practice guidelines for IBS are also in support of this treatment pathway. For example, the 2021 IBS treatment guidelines from the British Society of Gastroenterology and Romanian Society of Neurogastroenterology suggest tackling diet first, administering probiotics second, and using antimicrobials third [19, 20].
Let’s look at the two steps you should take before considering antimicrobials.
Eat healthily and make diet improvements that will help reset your gut health in a positive way.
Supplement with high-quality probiotics to help support your ongoing gut health.
Resetting the Gut With Healthy Diet
A healthy diet is so fundamental because it can reduce gut inflammation, which in turn can resolve imbalances in gut bacteria [21, 22].
I recommend starting with a Paleo diet, which removes or minimizes many potentially inflammatory foods such as gluten, dairy, chemical additives, and sugar. The Paleo diet has been shown to reduce inflammation by minimizing exposure to foods that may provoke an immune response .
However, if your gut issues are more entrenched, and you don’t see an improvement after a few weeks, a diet that eliminates a wider variety of troublesome foods may be needed, such as a low FODMAP diet.
It can take a few weeks to find a diet you’re happy with and enjoy that makes you feel healthier. At any point along this journey, you can also consider adding probiotics for more gut support.
Supporting Gut Health With Probiotics
Probiotics can help support your gut health by balancing out the gut microbiome.
One study found probiotics to be more successful than the antibiotic metronidazole in treating SIBO.
Probiotics support a healthy immune response in the gut, as well as reduce gut inflammation [24, 25, 26, 27].
Some research shows that probiotics may help prevent or treat viral infections, such as upper respiratory tract infections .
Take a quality blend of probiotics rather than just one type. At the Ruscio Institute for Functional Medicine clinic we’ve found a mix of three types — a Lactobacillus/Bifidobacterium blend, Saccharomyces boulardii (a friendly yeast), anda soil-based probiotic — to be particularly helpful
Monitor your symptoms for a month or so and notice when any improvements start to plateau.
Assuming you’ve achieved good benefits, you can start to taper down the amount of probiotics you take. Your aim is to find, and stay, on the minimum effective dose.
Moving Onto Antimicrobials
If you’re still getting some stubborn gut symptoms after making changes to your diet and taking probiotics, this is the point at which antimicrobials can be introduced.
For many people a herbal or plant-based antimicrobial product will effectively knock out any remaining pathogens that are contributing to ongoing symptoms. A broad-spectrum supplement is a good choice. You may also want to rotate the antimicrobials you use over time, as this has been shown effective in conditions such as SIBO .
When weighing herbal antimicrobials vs. antibiotics of the conventional type, remember pharmaceuticals can sometimes still win. It’s something you should discuss with a trusted health professional to find what’s right for you.
Antibiotics are usually a short course, but herbal antimicrobials are most often taken over a longer period of time (a few months).
Probiotics and Antibacterials Work Together
You may have heard that probiotics and antibiotics don’t mix, but this isn’t true.
Research is actually supportive of antibacterials/antibiotics being taken together with probiotics. For example:
Probiotics and antibiotics used together to treat SIBO increased the effectiveness of treatment . In one study, the two together were doubly effective compared with an antibiotic on its own .
In people with H. pylori, those who took probiotics and antibiotics together had better results than taking only antibiotics .
That said, it’s probably good practice to take these two categories of gut supplements at different times of day. You don’t want to give antimicrobials a chance to knock out the probiotics you’re taking.
Antimicrobial vs. Antibiotic: A Recap
Substances that kill a broad spectrum of microbes are antimicrobials, while those that only kill bacteria are antibiotics.
Broad spectrum, plant-based (herbal) antibacterials can be particularly helpful when it comes to ridding the gut of various unhelpful bacteria, viruses, and parasites that may slow your return to good health.
However, you don’t necessarily want to take antimicrobials straight away — try an anti-inflammatory diet and probiotics first, only introducing the antimicrobial supplement if you still have symptoms.
If you need help weighing the various antimicrobial vs. antibiotic agents, or with gut or wider health issues in general, you can schedule an appointment with one of our functional health practitioners, or read my book, Healthy Gut, Healthy You, for more guidance.
The Ruscio Institute has developed a range of high-quality formulations to help our patients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you.
Purssell E. Antimicrobials. In: Hood P, Khan E, editors. Understanding pharmacology in nursing practice. Cham: Springer International Publishing; 2020. p. 147–65. DOI: 10.1007/978-3-030-32004-1_6.
Ionescu MI. Are herbal products an alternative to antibiotics? In: Kırmusaoğlu S, editor. Bacterial pathogenesis and antibacterial control. InTech; 2018. DOI: 10.5772/intechopen.72110.
Scarpellini E, Giorgio V, Gabrielli M, Filoni S, Vitale G, Tortora A, et al. Rifaximin treatment for small intestinal bacterial overgrowth in children with irritable bowel syndrome. Eur Rev Med Pharmacol Sci. 2013 May;17(10):1314–20. PMID: 23740443.
Shah SC, Day LW, Somsouk M, Sewell JL. Meta-analysis: antibiotic therapy for small intestinal bacterial overgrowth. Aliment Pharmacol Ther. 2013 Oct;38(8):925–34. DOI: 10.1111/apt.12479. PMID: 24004101. PMCID: PMC3819138.
Hirschl AM, Rotter ML. Amoxicillin for the treatment of Helicobacter pylori infection. J Gastroenterol. 1996 Nov;31 Suppl 9:44–7. PMID: 8959518.
Anand U, Jacobo-Herrera N, Altemimi A, Lakhssassi N. A comprehensive review on medicinal plants as antimicrobial therapeutics: potential avenues of biocompatible drug discovery. Metabolites. 2019 Nov 1;9(11). DOI: 10.3390/metabo9110258. PMID: 31683833. PMCID: PMC6918160.
Hawrelak JA, Wohlmuth H, Pattinson M, Myers SP, Goldenberg JZ, Harnett J, et al. Western herbal medicines in the treatment of irritable bowel syndrome: A systematic review and meta-analysis. Complement Ther Med. 2020 Jan;48:102233. DOI: 10.1016/j.ctim.2019.102233. PMID: 31987249.
Tan N, Gwee KA, Tack J, Zhang M, Li Y, Chen M, et al. Herbal medicine in the treatment of functional gastrointestinal disorders: A systematic review with meta-analysis. J Gastroenterol Hepatol. 2020 Apr;35(4):544–56. DOI: 10.1111/jgh.14905. PMID: 31674057.
Black CJ, Yuan Y, Selinger CP, Camilleri M, Quigley EMM, Moayyedi P, et al. Efficacy of soluble fibre, antispasmodic drugs, and gut-brain neuromodulators in irritable bowel syndrome: a systematic review and network meta-analysis. Lancet Gastroenterol Hepatol. 2020;5(2):117–31. DOI: 10.1016/S2468-1253(19)30324-3. PMID: 31859183.
Hu Q, Peng Z, Li L, Zou X, Xu L, Gong J, et al. The Efficacy of Berberine-Containing Quadruple Therapy on Helicobacter Pylori Eradication in China: A Systematic Review and Meta-Analysis of Randomized Clinical Trials. Front Pharmacol. 2019;10:1694. DOI: 10.3389/fphar.2019.01694. PMID: 32116685. PMCID: PMC7010642.
Chedid V, Dhalla S, Clarke JO, Roland BC, Dunbar KB, Koh J, et al. Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth. Glob Adv Health Med. 2014 May;3(3):16–24. DOI: 10.7453/gahmj.2014.019. PMID: 24891990. PMCID: PMC4030608.
Mosaffa-Jahromi M, Lankarani KB, Pasalar M, Afsharypuor S, Tamaddon A-M. Efficacy and safety of enteric coated capsules of anise oil to treat irritable bowel syndrome. J Ethnopharmacol. 2016 Dec 24;194:937–46. DOI: 10.1016/j.jep.2016.10.083. PMID: 27815079.
Ng SC, Lam YT, Tsoi KKF, Chan FKL, Sung JJY, Wu JCY. Systematic review: the efficacy of herbal therapy in inflammatory bowel disease. Aliment Pharmacol Ther. 2013 Oct;38(8):854–63. DOI: 10.1111/apt.12464. PMID: 23981095.
Shinjyo N, Parkinson J, Bell J, Katsuno T, Bligh A. Berberine for prevention of dementia associated with diabetes and its comorbidities: A systematic review. J Integr Med. 2020 Mar;18(2):125–51. DOI: 10.1016/j.joim.2020.01.004. PMID: 32005442.
Kennedy D, Okello E, Chazot P, Howes M-J, Ohiomokhare S, Jackson P, et al. Volatile Terpenes and Brain Function: Investigation of the Cognitive and Mood Effects of Mentha × Piperita L. Essential Oil with In Vitro Properties Relevant to Central Nervous System Function. Nutrients. 2018 Aug 7;10(8). DOI: 10.3390/nu10081029. PMID: 30087294. PMCID: PMC6116079.
Beba M, Djafarian K, Shab-Bidar S. Effect of Berberine on C-reactive protein: A systematic review and meta-analysis of randomized controlled trials. Complement Ther Med. 2019 Oct;46:81–6. DOI: 10.1016/j.ctim.2019.08.002. PMID: 31519292.
Vasant DH, Paine PA, Black CJ, Houghton LA, Everitt HA, Corsetti M, et al. British Society of Gastroenterology guidelines on the management of irritable bowel syndrome. Gut. 2021 Jul;70(7):1214–40. DOI: 10.1136/gutjnl-2021-324598. PMID: 33903147.
Dumitrascu DL, Baban A, Bancila I, Barboi O, Bataga S, Chira A, et al. Romanian guidelines for nonpharmacological therapy of IBS. J Gastrointestin Liver Dis. 2021 Jun 18;30(2):291–306. DOI: 10.15403/jgld-3581. PMID: 33951120.
Lupp C, Robertson ML, Wickham ME, Sekirov I, Champion OL, Gaynor EC, et al. Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. Cell Host Microbe. 2007 Aug 16;2(2):119–29. DOI: 10.1016/j.chom.2007.06.010. PMID: 18005726.
Nistal E, Caminero A, Herrán AR, Arias L, Vivas S, de Morales JMR, et al. Differences of small intestinal bacteria populations in adults and children with/without celiac disease: effect of age, gluten diet, and disease. Inflamm Bowel Dis. 2012 Apr;18(4):649–56. DOI: 10.1002/ibd.21830. PMID: 21826768.
Whalen KA, McCullough ML, Flanders WD, Hartman TJ, Judd S, Bostick RM. Paleolithic and Mediterranean Diet Pattern Scores Are Inversely Associated with Biomarkers of Inflammation and Oxidative Balance in Adults. J Nutr. 2016 Jun;146(6):1217–26. DOI: 10.3945/jn.115.224048. PMID: 27099230. PMCID: PMC4877627.
Toribio-Mateas M. Harnessing the power of microbiome assessment tools as part of neuroprotective nutrition and lifestyle medicine interventions. Microorganisms. 2018 Apr 25;6(2). DOI: 10.3390/microorganisms6020035. PMID: 29693607. PMCID: PMC6027349.
Stenman LK, Lehtinen MJ, Meland N, Christensen JE, Yeung N, Saarinen MT, et al. Probiotic With or Without Fiber Controls Body Fat Mass, Associated With Serum Zonulin, in Overweight and Obese Adults-Randomized Controlled Trial. EBioMedicine. 2016 Nov;13:190–200. DOI: 10.1016/j.ebiom.2016.10.036. PMID: 27810310. PMCID: PMC5264483.
Leblhuber F, Steiner K, Schuetz B, Fuchs D, Gostner JM. Probiotic Supplementation in Patients with Alzheimer’s Dementia – An Explorative Intervention Study. Curr Alzheimer Res. 2018;15(12):1106–13. DOI: 10.2174/1389200219666180813144834. PMID: 30101706. PMCID: PMC6340155.
Frei R, Akdis M, O’Mahony L. Prebiotics, probiotics, synbiotics, and the immune system: experimental data and clinical evidence. Curr Opin Gastroenterol. 2015 Mar;31(2):153–8. DOI: 10.1097/MOG.0000000000000151. PMID: 25594887.
Hao Q, Dong BR, Wu T. Probiotics for preventing acute upper respiratory tract infections. Cochrane Database Syst Rev. 2015 Feb 3;(2):CD006895. DOI: 10.1002/14651858.CD006895.pub3. PMID: 25927096.
Ghoshal UC. Antibiotic treatment for small intestinal bacterial overgrowth: Is a cocktail better than a single? United European Gastroenterol J. 2021 Jul;9(6):643–4. DOI: 10.1002/ueg2.12075. PMID: 33951351. PMCID: PMC8280792.
Greco A, Caviglia GP, Brignolo P, Ribaldone DG, Reggiani S, Sguazzini C, et al. Glucose breath test and Crohn’s disease: Diagnosis of small intestinal bacterial overgrowth and evaluation of therapeutic response. Scand J Gastroenterol. 2015 May 19;50(11):1376–81. DOI: 10.3109/00365521.2015.1050691. PMID: 25990116.
García-Collinot G, Madrigal-Santillán EO, Martínez-Bencomo MA, Carranza-Muleiro RA, Jara LJ, Vera-Lastra O, et al. Effectiveness of Saccharomyces boulardii and Metronidazole for Small Intestinal Bacterial Overgrowth in Systemic Sclerosis. Dig Dis Sci. 2020 Apr;65(4):1134–43. DOI: 10.1007/s10620-019-05830-0. PMID: 31549334.
Wang F, Feng J, Chen P, Liu X, Ma M, Zhou R, et al. Probiotics in Helicobacter pylori eradication therapy: Systematic review and network meta-analysis. Clin Res Hepatol Gastroenterol. 2017 Sep;41(4):466–75. DOI: 10.1016/j.clinre.2017.04.004. PMID: 28552432.
I care about answering your questions and sharing my knowledge with you. Leave a comment or connect with me on social media asking any health question you may have and I just might incorporate it into our next listener questions podcast episode just for you!
Transform your health
Every product is science-based, validated by real-world use, and personally vetted by Dr. Ruscio, DC.