Plant Based Antimicrobials – How to Heal SIBO and other chronic GI Imbalances with Botanical Medicines
Unfavorable balance of microflora in our GI tract can wreak havoc on our health.1 Digestive disturbances like constipation or loose stools, bloating, gas, and pain, as well as systemic consequences of intestinal permeability such as autoimmune activation and inflammation, can often be traced to imbalanced intestinal ecology. The disadvantages of using pharmaceutical agents are commonly known, regarding the potential for further damage to the delicate beneficial species that help make up a healthy microbiome. So, are there any alternative options to help clear the unfriendly residents? Many practitioners find that specific well-balanced botanical blends can correct intestinal ecology without “throwing the baby out with the bathwater” the way that many other antimicrobial agents can.2
How Do Botanicals Work
There are many categories of antimicrobial herbs, some with high berberine alkaloid content like Gentian and Goldenseal, and some like Garlic that contains allicin and other compounds that have been extensively studied for potential effectiveness in resolving bacterial and fungal infections.3-5 Many essential oils exhibit antimicrobial activity, and several categories of antimicrobial herbal constituent compounds such as plant tannins, eugenols, and OPC’s can disrupt the development of biofilms through one of several mechanisms.6 Biofilm is the coating that bacteria and other pathogens develop to protect themselves from detection by our immune system and is a contributing factor to the recurrence of infection as well as the progression of many chronic illnesses.7,8
Biofilms are one of the main mechanisms by which pathogenic infections can become chronic or recur (think sinus infections, Candidiasis, UTI’s or children’s ear infections). When present, the secreted biofilm “shield” makes them up to one thousand times more resistant to antibiotic therapy. Pathogenic biofilms also trigger a much smaller host immune response than their planktonic counterparts. The advantage of broad-spectrum combinations of herbal ingredients is that they can break down and eliminate these biofilms through multifactorial biofilm-disrupting activity. They can inhibit Quorum Sensing, the communication which pathogens use to coordinate to build and maintain biofilm; they can prevent adherence of biofilm to the tissue; they can inhibit swarming motility of pathogens, and they can eradicate the pathogens themselves.9-11 A key factor is the ability to disrupt the Efflux Pump mechanism of pathogenic microbial self-preservation, which is one primary cause of drug resistance.12
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. 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.13
This passage outlines one important mechanism by which “borrowing” plants’ immune systems (by taking herbal supplements) activates and supports the human’s innate immune response. This is a critical point to understand when selecting herbal nutritional supplements to support healthy and balanced immune response.
In the follow-up tests, it is observed that the number and diversity of beneficial flora have increased over the course of the protocol, although no supplemental probiotics are given. It has also been noted that the pathogenic overgrowths are eliminated and that the sIgA marker for immune health has normalized in almost all patients.14 Although most herbal antimicrobial compounds cause damage to beneficial organisms as well as pathogens over time, it has been observed through this ongoing trial that when the Biocidin® combination is used long-term, it maintains a selectivity for pathogens that does not negatively impact the beneficial flora to an observable degree. We look forward to collating, analyzing and presenting the data from this ongoing research project as soon as possible. In a 2013 non-published university trial examining the effect of Biocidin® on biofilms, the Biocidin® combination showed effectiveness in dismantling and completely inhibiting the growth of all bacterial and fungal organisms and biofilms tested, including those generated by the common stubborn pathogens Pseudomonas aeruginosa, E. coli, and Candida albicans.15 Another yet unpublished university trial in 2016 found that the Biocidin® combination showed effectiveness in dismantling and completely halting all growth of Borrelia (Lyme) organisms in all of their pleomorphic forms including spirochetes, blebs, round bodies, and biofilms. The MIC® of Biocidin was found to be a 1:10 when used alone, and lower when used in conjunction with antibiotic drugs such as Ceftriaxone and Doxycycline.16 These results speak to the potential for antibiotic treatment synergy in cases of chronic infection due to the high degree of antimicrobial nutritional support that Biocidin® can be expected to confer when addressing Lyme borreliosis, and other common pathogens that generate or inhabit biofilm structures. We look forward to sharing this study when it is published, and we make the preliminary report data available to health care practitioners upon request.*
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 natural food or supplement store formulas, so more is not better. A gradual increase in dosage from a very small starting amount is advised, unless you are dealing with an acute issue. Your practitioner will tailor the increase in usage over time to your particular situation.
- There may be a die-off or Herxheimer-type reaction, so you may need tools to “mop up” pro-inflammatory byproducts of biofilm breakdown. We use a specialized clay and charcoal blend called G.I. Detox + to accomplish this. You may also need to be on a therapeutic diet in order to return to a healthy balance. Many use a low FODMAP or similar fermentable-saccharide and trigger-food-eliminating diet for this reason.
- Working with a Functional Medicine, integrative, or naturopathic practitioner is often helpful in order to pinpoint the culprit through thorough initial lab testing and follow up. Your practitioner can also provide specific 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 values to normalize. For instance, although 70% of SIBO patients reported symptoms greatly improved or completely resolved after the Biocidin® protocol was used in our 8-week SIBO pilot study, lab values of hydrogen and methane in the breath test still showed a need to continue for longer than the 8-week trial period in order to complete the pathogen clearance and avoid symptom recurrence. Some may need to continue to monitor their diet and we recommend the use of the Bioclear Cleansing Program product bundle annually to ensure that the system stays in optimal balance.
- These botanical nutritional supplements are not meant to cure, treat, or prevent any disease. They are very commonly used as a nutritional support during treatment but are not meant to replace any medically accepted treatment plan. They are designed for use under the supervision of a qualified healthcare practitioner.
The benefits of following a comprehensive cleansing supplement program like the one offered by Bio-Botanical Research are reported to be a better balance of energy/stress, better mental clarity, and reduced pain. The ultimate goal of such a protocol is getting the patient to a place in which they can enjoy vitality and health while living life to their fullest potential. The five formulas in our Comprehensive Cleansing Program are designed to work together to provide a well-balanced regime that is as broad-spectrum, easy to use, and as comfortable as possible.
Comprehensive Cleansing Program
Biocidin® or Biocidin® LSF – Broad spectrum antimicrobial herbal combination used to address both GI-local and global/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 extract 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 + – A powerful binding agent blend to mop up and remove toxins, which can help lessen die-off or Herxheimer-type reactions. Ingredients: Zeolite clay, activated charcoal, Aloe Vera, MMST Silica, apple pectin, Humic/Fulvic acid blend.
Proflora 4R™ – Restorative Probiotic Combination with Spore forming strain and botanicals to assist in repairing the intestinal lining. Ingredients: 3 Billion Spore Forming Cells (Bacillus subtilis, HU58™, Bacillus coagulans, Bacillus clausii), Quercetin (Patented form QU995 is 170 times more bioavailable than regular quercetin), Marshmallow Root, Aloe Vera 200:1 extract.
Biotonic™ – Adaptogenic and digestive tonifying combination of traditional Chinese herbs (organically grown and tested for purity) which supports nutrient absorption and HPA axis balance without common adaptogenic nightshade herbs. Ingredients: Astragalus, Sweet Wormwood, Eleuthero Ginseng, Chinese Knotweed, Ginger, Wild Yam, Atractylodes, Poria Mushroom, Codonopsis, Peony, Curcuma, Tangerine Peel, Licorice Root.
Where to Get Biocidin®
Healthcare professionals interested in Biocidin can reach out for more information at firstname.lastname@example.org.
- Carding S, Verbeke K, Vipond DT, Corfe BM, Owen LJ. Dysbiosis of the gut microbiota in disease. Microb Ecol Health Dis. 2015;26:26191.
- 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.
- 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.
- Wu, X., Santos, R. R., & Fink-Gremmels, J. (2015). Analyzing the antibacterial effects of food ingredients: model experiments with allicin and garlic extracts on biofilm formation and viability of Staphylococcus epidermidis. Food Science & Nutrition, 3(2), 158–168. http://doi.org/10.1002/fsn3.199
- Shuford JA, Steckelberg JM, Patel R. Effects of fresh garlic extract on Candida albicans biofilms. Antimicrob Agents Chemother. 2005;49(1):473.
- Kim, Y.-G., Lee, J.-H., Gwon, G., Kim, S.-I., Park, J. G., & Lee, J. (2016). Essential Oils and Eugenols Inhibit Biofilm Formation and the Virulence of Escherichia coli O157:H7. Scientific Reports, 6, 36377. http://doi.org/10.1038/srep36377
- Davey ME, O’toole GA. Microbial biofilms: from ecology to molecular genetics. Microbiol Mol Biol Rev. 2000 Dec;64(4):847-67.
- Bjarnsholt T. The role of bacterial biofilms in chronic infections. APMIS Suppl. 2013 May;(136):1-51. doi: 10.1111/apm.12099.
- Huber B, Eberi L, Feucht W, Polster J. Influence of polyphenols on bacterial biofilm formation and quorum-sensing. Z Naturforsch C. 2003 Nov-Dec;58(11-12):879-84.
- Gupta PD, Birdi TJ. Development of botanicals to combat antibiotic resistance. Journal of Ayurveda and Integrative Medicine 2017;8(4):266–275.
- Kavanaugh Nl, Ribbeck K. Selected antimicrobial essential oils eradicate Pseudomonas spp. and Staphylococcus aureus biofilms. Appl Environ Microbiol. 2012 Jun;78(11):4057-61.
- Aghayan SS, Mogadam HK, Fazli M, et al. The Effects of Berberine and Palmatine on Efflux Pumps Inhibition with Different Gene Patterns in Pseudomonas aeruginosa Isolated from Burn Infections. Avicenna Journal of Medical Biotechnology. 2017;9(1):2-7.
- 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.
- De Haas J. Data collection method for determining the impact of Biocidin botanical formula on GI tract microbiota. Haarlem (Netherlands): For Balance Clinic; 2017 Jun. Preliminary Report No.: SB02. Contract No.: NA. Sponsored by Bio-Botanical Research Inc.
- Marques C. Preliminary Report on Activity of Biocidin against Multiple Species of Biofilms. Binghamton (NY). Binghamton University, Biological Sciences Department; 2016 Mar. Preliminary Report No.: BFP01. Contract No.: NA. Sponsored by Bio-Botanical Research Inc.
- Gilbert L. Preliminary Report on Activity of Biocidin against Borrelia Species. Jyväskylä (Finland). University of Jyväskylä, Biological and Environmental Science Department; 2017 Apr. Preliminary Report No.: BBS03. Contract No.: NA. Sponsored by Bio-Botanical Research Inc.
Dr. Rachel Fresco, L. Ac., Ph. D.
Her focus has been on concerns relating to infection, and the digestive and immune systems. University-based research on her formulas includes studies on Lyme disease, biofilms and immune response. Informal clinical trials using the formulas are ongoing, examining activity against SIBO, H. Pylori, Dental Infections and Candida.
Many noted authors, physicians and laboratories recommend the broad-spectrum formulations such as the Biocidin®, Olivirex®, and GI Detox® she developed along with her team of scientists and formulators.
From what I’ve read, Biocidin is a pretty broad-spectrum anti-microbial, meaning it’s not that targeted and will kill a lot of good bacteria. Your thoughts?
Patty, in general, using botanicals such as Biocidin will do some global killing, but much less so than antibiotics. And whole plants provide nourishment for the microbiome as well. In general, I am not too concerned about botanical damage. Of course, if we use isolated botanical constituents at higher doses (behaving on unlike medications), we need to pay attention
Hi! I’m considering using GI detox as part of my sibo treatment plan. I do see that the ingredients include aloe vera and apple pectin, which both are on my no list for sibo because they are highly fermentable. Do you have any thoughts on whether the amount of the aloe vera and apple pectin are so small that it won’t make a difference? Thanks so much!
The answer to that will vary from one individual to another. We find our more sensitive SIBO patients will not tolerate supplements containing aloe vera, apple pectin, marshmallow root (among others) often found in GI restoration formulas. Often we begin our GI protocol with antimicrobials (prescription or botanical as indicated) then shifting to gut healing phase where we use these botanicals. You can learn more about our 6R approach on this blog: https://www.drkarafitzgerald.com/2017/05/31/our-6r-program-six-steps-to-save-your-health-through-your-gut/
I would also recommend working under the guidance of a Functional Medicine practitioner to accurately diagnose and treat the full picture
Hi Dr Fitzgerald! Love your work and your podcasts!
In the treatment of SIBO, whether using an antibiotic or herbal formula such as biocidin, when would you take the GI detox to prevent herxheimer reactions? One hour before or one hour after taking antimicrobials?
Maybe a better question is how long is the duration of action of the binder? I’m thinking I want the binder to be downstream to catch toxins when one takes the antimicrobial, right?
Thank you in advance!
Thank you for following!
Yes! You want to separate the binder from everything as far as possible (and recommend extra hydration). Keeping in mind individual variations in transit time, I think at least 2 hours from antimicrobials, and food or other nutrients. Depending on the product, the company may have additional details or research on the use and timing of their products.
Hi, how long do you think biocidin will take to work for gut dysbiosis caused on poor diet?
Hi Angel, great question and the answer is, it depends on what is causing the dysbiosis and a poor diet can exacerbate GI symptoms. A general timeline can be 60-90 days.
Is there a liquid biocidin that is FREE of walnut. Walnut is an allergic response in some. And does cause anaphylaxis is some. It kills bacteria, so I’m assuming it kills the good as well? If you have data to shiw otherwise, can you share it? Being it broad spectrum is there a list of the amount/percent of each ingredient contains in this spectrum?
Hi Tamara, there currently isn’t a Biocidin formula that is walnut/nut free at this time. The Biocidin team did a pilot study looking at pre/post stool samples of 13 individuals who took Biocidin liquid and G.I. Detox for 8 weeks, and found that their beneficial bacteria either stood still or increased, suggesting that this product does not harm the beneficial bacteria of the gut.
I am currently using Biocidin and Olivirex to treat bacteria overgrowth and parasites.
I have tried to introduce ProFlora 4R but experienced some digestive side effects on a low initial 1/4 capsule dose (nausea / indigestion / painful bloating). My practitioner recommended I stop the product immediately. I just wondered whether these side effects are common, and whether they would settle down with continued use?
In our experience, Proflora is generally well-tolerated. But with some cases of SIBO, probiotics can trigger some symptoms. We usually continue with the antimicrobials and motility agents a little longer.
You may find this article our team authored on our SIBO approach useful https://www.ifm.org/news-insights/managing-sibo-dietary-interventions/
This is really very informative.I have started taking Olivirex and Biocidin as recommended by the Functional Med.Doctor that I’m working with due to dysbiosis.I’m just thinking that I can likewise ask questions if needed.
Hello Marilyn, my apologies for the delayed response. We are monitoring these questions more carefully now, and would be happy to respond to you.
My functional med doc wants me to take Biocidin and Oliverex for H. pylori and other bad bacteria. However, I am allergic to walnuts. Is there a nut-free substitute for Biocidin?
Hi there. We can’t recommend specific products, but something to keep in mind is that each of the botanicals contained in both Biocidin liquid and Olivirex have been shown to have antimicrobial properties. Your FxMed doc might be able to help you find alternatives that do not contain black walnut, whether it is combination products or a mix of stand alone botanicals.
What product in the Biocidin line helps with motility?
Hello Chris! Both the Proflora and the GI Detox contain aloe, which can support motility.
Does this product help or hinder people with hydrogen sulfide/thiol intolerance issues as it contains garlic etc ?
Dear Dr. Fitzgerald,
It is an honor to be able to connect with you here! I love Biocidin, and greatly appreciate your work!
I am seeking your opinion about the potential for bacterial and/or viral resistance to herbs. I have read that Biocidin can be used safely once or even twice per year, for 4-8 weeks each time, for a cleanse.
When kept to those limits (used no more than twice per year), it appears Biocidin does not pose a risk of bacterial or viral resistance. Does that sound accurate? May I ask your opinion on that?
I see a functional medicine practitioner, and we have twice used Biocidin to treat SIBO. Last treatment was spring of this year, 2022. I only took it 5 mins before meals, however, at a daily dose of 15 drops (5 drops, 3x day) for 2 months. I’m just now seeing I should have better taken it 20 mins before meals, and it looks like dosage is more supposed to be 30 drops/day. So I’m kind of kicking myself, because I’m feeling those bubbles again, and lately having to exist on a low-FODMAP diet again.
Any pearls of wisdom appreciated. Happy holidays to you and yours!
Thanks for your comment! In general, it is much harder for pathogens to develop resistance to complex herbals such as used in Biocidin and others. That said, we do often use a rotation of different products for SIBO.
– Team DrKF