Plant Based Antimicrobials – How to Heal SIBO and GI Dysbiosis with Botanical Medicines

DrR Post Botanicals

There are many categories of antimicrobial herbs, some with compounds that are researched for effectiveness in bacterial and fungal infection.3 Many essential oils are also antimicrobial, and almost all antimicrobial herbs have an effect on disrupting biofilms, the coating that bacteria and other pathogens develop to protect themselves from detection by our immune system.

Plant Based Antimicrobials – How to Heal SIBO and GI Dysbiosis with Botanical Medicines

*Thank you to Bio-Botanical Research for providing the article*

Unfavorable balance of microflora in our GI system can wreak havoc on our health.1 Digestive disturbances like constipation or loose stools, bloating, gas, and pain, as well as systemic consequences of leaky gut such as autoimmune diseases and inflammation all be traced to imbalanced intestinal ecology. “Mastering the gut”, as Dr. Ruscio puts it, is the key to almost every chronic illness.

The risks of using pharmaceutical agents are commonly known, in terms of the potential for further damage to our microbiome, so what are our options to deal with the unfriendly residents? Many practitioners find that plant-based medicines can correct our intestinal ecology without “throwing the baby out with the bathwater” so to speak. 2

How Do Botanicals Work

There are many categories of antimicrobial herbs, some with high Berberine content like Gentian and Goldenseal, some with Garlic that have allicin and other compounds that are researched for effectiveness in bacterial and fungal infection.3 Many essential oils are also antimicrobial, and almost all antimicrobial herbs have an effect on disrupting biofilms, the coating that bacteria and other pathogens develop to protect themselves from detection by our immune system.4


Biofilms are one of the main reasons why infections become chronic or recur, (think sinus infection, Candida, UTI’s or children’s ear infections for example) and biofilms also make them resistant to antibiotics. The advantage of broad-spectrum combinations of plants is that they disrupt and eliminate these biofilms by inhibiting Quorum Sensing, one of the ways biofilms begin to form; they stop them from adhering to surfaces, and they eradicate the bacteria within the biofilm. A key factor is the ability to disrupt the Efflux Pump mechanism, which is the cause of antibiotic resistance.

The Research

According to research presented in the Int. Journal of Molecular Sciences in 2009:

Plants have developed defense mechanisms to a variety of pathogens. Some plant metabolites represent constitutive chemical barriers to microbial attack (phytoanticipins) and others are inducible antimicrobials (phytoalexins). They are extensively studied as promising plant and human disease-controlling agents. 5

The antimicrobial plant compounds that have received more attention in plant defense are the phytoalexins. Phytoalexins are antimicrobial compounds which require de novo expression of the enzymes involved in their biosynthetic pathways after elicitation. Therefore, the production of phytoalexins requires transcriptional and/or translational activity in the plant once the pathogen has been detected. The induced response mechanism also involves the trafficking and secretion of antimicrobial compounds to the infection site.5

The term phytoanticipin refers to ‘low molecular weight antimicrobial compounds that are present in plants before challenged by microorganisms or are produced after infection solely from preexisting constituents.’5

Bio-Botanical Research

BioBotanica ResearchAt Bio-Botanical Research we have spent the last 28 years developing formulations such as Biocidin® that have a broad-spectrum effect while sparing beneficial flora. In one research project at For Balance Clinic in the Netherlands, Dr. Jeroen De Haas tested over 1000 patients by stool analysis that were to be given Biocidin for gut dysbiosis. 6 In follow up tests the number and diversity of friendly flora increased during the course of treatment, even though no additional probiotics were given, and the problematic bacteria were eliminated. It was also noted that the SIgA marker for immune health had normalized. In two university studies on biofilms, the Biocidin® combination showed effectiveness on all bacterial and fungal biofilms, including Lyme. 6

What You Should Know About Using Botanicals

There are several important things to know before using professional strength botanicals. These are much more potent than health food or vitamin store formulas, and more is not better, so a gradual increase of dosage is advised unless you are dealing with an acute issue. Even so,

  • There may be a die-off or herxheimer reaction, so you may need tools to “mop up” toxins. (We use a specialized clay and charcoal blend called GI Detox to accomplish that)
  • You may need to be on a special diet to help your GI system return to a healthy balance. Many use a low FODMAP diet for this reason.
  • Working with a functional medicine, integrative or naturopathic practitioner will help to pinpoint the culprit through proper lab testing and follow up, provide dietary recommendations and will be able to make sure you get the support you need.

It may take 2-4 months or longer for lab tests to normalize, although 70% of SIBO patients reported symptoms greatly improved or gone in our study after 6-8 weeks. (Lab values of hydrogen and methane in the breath test still showed a need to continue for longer than 8 weeks for complete clearance and to avoid a relapse of symptoms.)

  • Some may need to continue to monitor their diet and we recommend use of the Comprehensive Program annually to be sure that your system stays in optimal balance.


The benefit of following a program like this, is that you can start feeling more energized, have better mental clarity, and experience reduced pain and inflammation. The ultimate goal is getting you to a place where you can enjoy vitality and health and living life to your highest potential.

The 5 formulas in our Comprehensive Cleansing Program are designed to work together to provide a well-balanced regime that is easy to use and is well tolerated.

Comprehensive Cleansing Program

The kit provides a 2-month supply of the following products:

Biocidin® – Broad spectrum antimicrobial botanical combination for that addresses both in the GI tract systemic challenges.   Ingredients – Bilberry extract, Noni, Milk Thistle, Echinacea, Goldenseal, Shiitake, White Willow Bark, Garlic, Grapeseed extract, Black Walnut, Raspberry, Fumitory, Gentian, Tea Tree oil, Galbanum oil, Lavender oil, Oregano oil.

Olivirex® – High Potency Olive Leaf combination with a synergistic combination of botanicals to assist detoxification and support the body’s defenses. Ingredients –

375 mg Olive Leaf extract (organic, minimum 18-24% oleuropein content), 125 mg combination of the following: Garlic, Goldenseal, Milk Thistle, St. John’s Wort, Uva Ursi, American Ginseng, Bladderwrack, Cordyceps, Dandelion, Noni,  White Willow Bark.

GI Detox™ – Pyrophyllite clay and activated charcoal blend top mop up and remove toxins, helps prevent die-off or Herxheimer reactions.

Proflora 4R™ – Restorative Probiotic Combination with Spore forming strain and botanicals to assist in repairing the gut.  Ingredients – 3 Billion Spore Forming Cells (Bacillus subtilis, HU58™, Bacillus coagulans, Bacillus clausii), Quercetin (Patented form QU995 is 170 x’s more bioavailable and great for histamine reduction), Marshmallow Root, Aloe Vera 200:1 extract.

Biotonic™ – Adaptogenic combination of traditional Chinese herbs (organically grown and tested for purity) which targets digestion, supports adrenal health and bolsters the body’s defenses.

Where to Get Biocidin

Patients, ask your health care practitioner about Biocidin and the Comprehensive Cleansing Program. Read more online at

Healthcare professionals interested in Biocidin, can reach out for more information and to set up Clinical Applications training at [email protected]

  1. Carding S, Verbeke K, Vipond DT, Corfe BM, Owen LJ. Dysbiosis of the gut microbiota in disease. Microb Ecol Health Dis. 2015;26:26191.
  2. Hawrelak JA, Cattley T, Myers SP. Essential oils in the treatment of intestinal dysbiosis: A preliminary in vitro study. Altern Med Rev. 2009;14(4):380-4.
  3. Wang, D.; Yu, L.; Xiang, H.; Fan, J.; He, L.; Guo, N.; Feng, H.; Deng, X. Global transcriptional profiles of Staphylococcus aureus treated with berberine chloride. FEMS Microbiol. Lett. 2008, 279, 217-225.
  4. Shuford JA, Steckelberg JM, Patel R. Effects of fresh garlic extract on Candida albicans biofilms. Antimicrob Agents Chemother. 2005;49(1):473.
  5. González-Lamothe R, Mitchell G, Gattuso M, Diarra MS, Malouin F, Bouarab K. Plant antimicrobial agents and their effects on plant and human pathogens. Int J Mol Sci. 2009;10(8):3400-19.
  6. Access to Bio-Botanical Research Studies is available within our healthcare provider portal, you can sign up here to learn more about the protocol as well as past and current research.

What do you think? I would like to hear your thoughts or experience with this.

Dr. Ruscio is your leading functional and integrative doctor specializing in gut related disorders such as SIBO, leaky gut, Celiac, IBS and in thyroid disorders such as hypothyroid and hyperthyroid. For more information on how to become a patient, please contact our office. Serving the San Francisco bay area and distance patients via phone and Skype.


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