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Antibacterial Treatment




Metronidazole antibiotic medication for SIBO treatmentFor The Treatment Of Bacterial Dysbiosis, Small Intestinal Bacterial Overgrowth (SIBO), Bacterial Overgrowth

The Problem

Bacterial dysbiosis is a common finding among environmental illness sufferers going by results from stool analysis, organic acid testing, hydrogen breath tests and gut fermentation profiles reported in lay literature. There is also a growing body of research linking small intestinal bacterial overgrowth (SIBO) with chronic fatigue syndrome, fibromyalgia and irritable bowel syndrome1, 2, 3.

Given these findings it's a good idea to have one or more of the lab tests mentioned above to determine if you have a bacterial overgrowth problem as treating this may improve your overall condition considerably.

Read more about these useful lab tests


Treating Bacterial Dysbiosis

There are many options available for treating bacterial dysbiosis but it generally boils down to a change in diet and/or taking an anti-bacterial agent along with probiotics/prebiotics.

All available research points to small intestinal bacterial overgrowth (SIBO) being the problem in environmental illnesses so we'll concentrate on this.



According to Dr. Leo Galland, a specialist in dysbiosis related illness, the best diet to aid in the treatment of SIBO is very similar to that used to treat yeast overgrowth. This being a diet free of simple sugars and grains/cereals and low in fruit and starchy vegetables depending on individual tolerance. This diet restricts the nutrition available for bacteria in the upper GI tract to proliferate and reduces the excess alcohols and organic acids that are produced as a result of bacterial fermentation.

See the anti-fungal page for more details on the low carb diet.


Anti-Microbial Treatment

There are basically two options when it comes to eradicating bacterial overgrowth, antibiotic medication or natural antibiotic substances. The two can be combined however and often are, to good effect. It usually takes a period of several months or more to get a bacterial overgrowth under control so the risk/benefit profile of potential treatment must be considered. For this reason the use of natural substances with fewer side-effects than medications is particularly appealing. There are a few specific medications that are commonly used in the treatment of SIBO and a huge number of natural substances that can potentially be used. We'll look at some of the most common medications and natural antibiotics in more detail now.


Antibiotic Medications

Antibiotic medications can be seen as a double-edged sword. They have the potential to both cause and treat intestinal bacterial overgrowth. When dealing with SIBO with antibiotic medications it is important to know how they will effect beneficial species of bacteria in the intestines. Some broad spectrum medications may cause more harm than good, wiping out more of the beneficial bacteria. For this reason, specific medications targetting only the pathogenic bacteria causing the problem are used as much as possible.

Metronidazole appears to be the drug of choice for treating most cases of SIBO judging by reports from physicians and the scientific literature. There have been a number of studies showing metronidazole to be effective in treating SIBO4, 5. Mitronidazole is extremely effective against anerobic bacteria but has little effect on aerobes. The most common side-effects of use involve the gastrointestinal tract with nausea being the most common and diarrhea and abdominal discomfort frequently occuring. Another side-effect listed is the subsequent growth of candida in the vagina, so it is safe to say candida growth in the intestines may present as well. When using mitronidazole or any other antibacterial it is important to use probiotics and possibly anti-fungal agents concurrantly to avoid candida overgrowth.

Although tetracycline is likely the cause of a large number of cases of both bacterial and fungal dysbiosis due to its broad spectrum of action killing of resident flora, it is sometimes necessary to use it in the treatment of SIBO if other more focused antibiotics aren't effective against an identified pathogen. It is especially important to reinoculate the intestines with friendly bacteria when tetracycline is used because of the way it indiscriminantly kills off friendly bacteria as well as the offending organisms.

Ciprofloxacin is the most common drug used when an overgrowth of aerobic bacteria such as enterobacter sp. or klebsiella oxytoca is present for example. Ciprofloaxacin is very specific and very powerful at killing aerobes while having no effect on anerobes. Side-effects from ciprofloaxacin encountered by patients in order of frequency are nausea (2.5%), diarrhea (1.6%), liver function tests abnormal (1.3%), vomiting (1.0%), and rash (1.0%). However, where dysbiosis patients are concerned GI and liver related side-effects due to the poor health of these organs/tissues could be of significant concern.


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Herbal/Natural Antibiotics

Natural antibiotics substances have a number of advantages over drug therapy. The two main ones being the lower incidence of side-effects and the cheaper cost of treatment. This is an important factor when you consider that treatment for SIBO can often take a long period of time. Here are some of the most common natural antibiotics used to treat SIBO.

Grapefruit Seed Extract (GSE)
This bitter herb is widely used by naturopaths and alternative minded doctors to treat SIBO and other GI infections. Lab testing has shown it to be effective against a long list of microorganisms including Giardia lamblia, Proteus vulgaris, E.coli, Aspergillus parasiticus, Salmonella typhi and Staphylococcus aureus. GSE is especially useful where infecting microbe cannot be determined as it is effective against such a wide range of pathogens. Another advantage is that it is effective for controlling diarrhea. GSE generally comes in either capsules, good if you can't stand the taste) or in liquid concentrate form. As low a dose as 2-4 drops in 4oz water or juice twice daily can be effective.

Garlic (Allium sativum)
Garlic is arguably the most famous natural antibiotic. In World War II it was used by the Russians to treat typhus, dysentry, septic poisoning and gangrene in batle wounds when they ran out of penicillin. This gained it the nickname 'Russian penicillin'. Garlic's antimicrobial activity is derived from several compounds, the most important of which is allicin. Studies have found garlic to be effective in combatiing infections with bacillus, brucella, citrobacter, E.coli, hafnia, klebsiella, Salmonella typhi, shigella, Vibrio chlorae and various species of staph and strep. Garlic can also be useful for relieving gas pains and as an antispasmodic. It is most effective when taken raw, either eaten with food or pressed into a juice. Many people find this isn't acceptable due to the taste/smell or the fact that it may sting the GI tract, especially if it is irritated. If this is the case it is available in capsules. To combat SIBO 2-3 capsules, 3 times daily would be a reasonable dose.

Research has shown that ginger possesses inhibitory action against a variety of pathogenic bacteria including Staphylococcus aureus, E.coli, Salmonella and Steptococcus viridans. Also of benefit in treating bacterial dysbiosis is the fact that ginger acts as a prebiotic, encouraging the growth of friendly bacteria like Lactobacilli sp. Ginger also has a number of other properties that make it beneficial for treating SIBO and associated problems. For instance ginger is known to be very high in anti-oxidants which will make it useful for reducing inflammation and other problems associated with the oxidative stress that is commonly seen in environmental illnesses6. Ginger has also been proven to be effective for treating nausea and vomiting from a variety of causes which is again relevant to bacterial dysbiosis and environmental illnesses7.

Olive Leaf Extract
Olive leaf extract has a broad antimicrobial action and is often used by alternative medicine practioners to treat gut dysbiosis, chronic fatigue syndrome and irritable bowel syndrome amongst other things. In one study olive leaf extract was shown to completely destroy E.coli cells at a very low concentration of only 0.6%8. Like ginger it has the benefit of promoting the growth of friendly bacteria as well as killing pathogenic bacteria due to its high content of fructooligosaccharides (FOS).

Peppermint, in the form of enteric coated capsules, has been shown in clinical studies to significantly improve IBS symptoms due to small bowel bacterial overgrowth. In one case study significant improvement was seen both in symptoms reported by the patient and on hydrogen breath analysis, indicating a decrease in small bowel bacteria1. Peppermint also has significant anti-oxidant activity6 and known to enhance digestion by increasing stomach acid production. Other benefits derive from its ability to slightly anesthetize mucous membranes thus making it useful for digestive problems in general by calming the GI tract. Specific problems that can benefit are nausea, indigestion and diarrhea.

The alkaloid berberine is the active compound found in goldenseal, oregon grape root, barberry and Chinese goldthread. It's included here seperately as it is commonly available as pure berberine extract. Berberine is a strong antibacterial and works by a unique mechanism. It appears to work by staining microbes to be targets for macrophages (large immune cells that 'eat' pathogens) and by preventing microbes from attaching to cells. Berberine has been widely studied and shown to have high antimicrobial activity, mainly against Gram-positive bacteria and yeasts9. It has been found to be most effective against S. aureus, P. aeruginosa S (sensitive), E. coli S, P. aeruginosa R (resistant), E. coli R10. Berberine is commonly used by doctors treating dysbiosis and is included on many microbial sensitivity tests carried out on stool samples by the major functional medicine labs.

Echinacea contains the antibiotic coumpound echinacoside which has broad spectrum activity and it often compared in potency to penicillin. This fact is well known in Germany where Echinacea is used to treat bronchitis, tonsilitis, ear infections, wounds and absecesses amongst other infectious diseases. As well as having powerful direct activity against a wide range of bacteria, echinacea is also a powerful immune-stimulator. It works to improve the body's defenses by three methods. Firstly it contains a substance known as echinacein that deactivates the tissue-dissolving enzyme used by bacteria to spread and infect other tissues, thus preventing them from doing so. Secondly echinacea has been shown in a well respected immunology journal to stimulate production of white blood cells and phagocytes and increase macrophage activity. Finally echinacea has the ability to significantly boost production of infection-fighting T-lymphocytes. Not only that but it was found to do this significantly better than many standard immune-supportive drugs. This herb is best taken in liquid or capsule form and should not be taken for longer than 8 weeks at a time. For treating SIBO it can be effective when rotated with some of the other natural antibacterials.



It is a good idea that as the bacterial overgrowth is being treated probiotic bacteria are consumed to take the place of the pathogenic colonies and prevent recurrence or overgrowth of yeast. To learn more about probiotics click here



Antibacterial TreatmentDynamic Neural Retraining Program (DNRS)


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