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Treating Harmful Bacteria

Because half of the stool tests I see show harmful bacteria and no yeast infection, and many times those bacteria have infected the small intestine, which is known as sibo, I thought it would be a very good idea to give you a plan to kill these bad bacteria.

The sibo treatment plan below is slightly different from the yeast infection treatment plan and is clinically proven to work. One plan is based on a clinical medical study, the other is based on what I see on stool test results.

If the bad bacteria is confined to the colon, the intestinal yeast treatment plan or the systemic plan will work just fine.

Common Harmful Bacteria

There are quite a few different species of harmful bacteria that can infect the human body so this is by no means a complete list. Depending upon what lab did the stool test, they may or may not be listed as a Possible Pathogen (PP). However, the bacteria in the list below are generally recognized by most labs as human pathogens and I quite often see them on stool test results.

Proteus mirabilis is a gram negative, anaerobic (anaerobic means it does not require oxygen for growth), rod shaped bacteria that causes 90% of all bacterial infections in humans. This harmful bacteria produces urease that form kidney stones. If the stones or the infection get bad enough, it can result in kidney failure.

harmful bacteria

Klebsiella pneumoniae is also a gram negative, anaerobic, rod shaped bacteria. It can ferment dairy foods and it likes sugar as a food source. It is commonly found in the intestine, mouth and skin. The most common infection it causes is pneumonia.

Enterobacter cloacae is another harmful bacteria that is gram negative, anaerobic and rod shaped. It quite often is the cause of urinary and respiratory tract infections.

Campylobacter species are gram negative but instead of being rod shaped they are shaped like corkscrews. Over a dozen of these species have been implicated in human diseases. These bacterial species often produce an inflammatory diarrhea that is often bloody if it gets bad enough. They can induce intestinal cramps, fever and pain.

Citrobacter species of bacteria are gram negative and also rod shaped but does not produce spores. These bacteria are found just about everywhere so it’s important to wash your hands after using the restroom or handling food.

Citrobacter freundii can cause brain abscesses, meningitis, gastrointestinal infection, inflammation, which include watery diarrhea with stomach pain, and sometimes blood in the stool. It thrives on FOS!

Citrobacter cloacae can give you respiratory and urinary tract infections.

Clostridium difficile is a gram positive bacteria that produces spore forming rods much like candida albicans hyphae. This bacteria is normally found in the intestine in small amounts. It usually gets out of control as a result of taking antibiotics that kill your good bacteria.

This harmful bacteria then causes diarrhea and can result in colitis. Colitis is a severe form of intestinal infection and results in diarrhea, bloating and severe abdominal pain. It can also give you flu like symptoms and inflammatory bowel disease. It’s resistant to most antibiotics and for folks over 65, it can be deadly… About one in nine people over 65 with C. difficile dies within 30 days.

E coli is the primary bacteria responsible for most urinary tract infections. In the gut, it can cause stomach cramps, nausea, vomiting and diarrhea. Sometimes the infected person won't notice any symptoms at all and may spread the bacteria to others. In severe cases, it can cause kidney failure.

Staphylococcus aureus is an anaerobic, gram positive bacteria that is responsible for what is commonly referred to as a staph infection. It is found on the skin and inside the nose. On the skin it can plug pores leading to acne and other skin infections. This harmful bacteria can also lead to other more serious diseases such as meningitis, toxic shock syndrome, osteomyelitis, pneumonia, endocarditis, bacterimia, chest pain and sepsis. It is a major pathogen in hospitals and is acquiring antibiotic resistance as time goes by.

Pseudomonas aeruginosa can infect both humans and animals. It is found everywhere, eats just about anything and commonly lives on the skin. People with reduced immune function are most susceptible to this harmful bacteria. It causes generalized inflammation but if it infects the lungs or the urinary tract and kidneys it can be fatal.

This harmful bacteria is extremely pathogenic, the wife and I have both been infected by it. Her infection was caused by a dog bite and within a week it had eaten a 2" pocket hole in her leg. I in my right eye and within days I could not see anymore.  Both of us recovered but we do have a little bit of long lasting scar tissue damage. It does build a biofilm.

This study done in 2011 by Ammons MC, Ward LS, Dowd S, James GA at the Center for Biofilm Engineering, Montana State University found that because it uses iron in its biofilm, lactoferrin in combination with xylitol helps clear the infection. Lactoferrin destabilizes the bacterial membrane by pulling iron from the biofilm, xylitol inhibits the ability of the bacteria to produce siderophores or reproduce.1

Combine this with Biofase, a biofilm buster, and herbs that a stool test show it is susceptible to, and you should be able to clear the infection fairly quick. If you don't have stool test results, use the protocol below.

Various streptococcus species, although most labs don't recognize these species as possible pathogenic bacteria, can cause problems if they over grow.

Like I said before, this is a very short list but I see these bacteria  quite often on stool test results. Most good stool tests will also run a susceptibility test to see what will kill these harmful bacteria.

Quite often these harmful bacteria will infect the small intestine as well, which is known as sibo. You can do this simple test for sibo to verify that's what you have or not.

Breath tests for sibo are not able to distinguish species, but according to a study published in May 2012, The bacteria that are most commonly overgrown are anaerobes (Bacteroides in 39%, Lactobacillus in 25%, and Clostridium in 20%) and aerobes (Streptococcus in 60%, Escherichia coli in 36%, Staphylococcus in 13%, and Klebsiella in 11%).2

In another study, the findings showed the over grown bacteria to be E coli in 37%, Enterococcus species in 32%, Klebsiella pneumoniae in 24%, and Proteus mirabilis in 6.5% of sibo cases.3

You could however do this stool test to get a better idea what you are infected with, and what would be the best things to take to get it under control. 

You could then see your doctor for the appropriate antibiotic and kill them that way if you choose to. However, this study points out that the herbs are just as effective for sibo as the antibiotics with a lot less side effects.4

Treatment times with natural compounds take twice as long as antibiotics, typically four weeks verses two weeks. If the antibiotics are the way you decide to go, I would at the very least, take Biofase while on the antibiotic to reduce the chance of yeast over growth and to reduce the bacterial biofilms, which will make the antibiotics more effective.

Harmful Bacteria Protocol

Looking at this published study from Global Advances in Health & Medicine in 2014,  we find that a 4 consecutive week treatment of herbs had a positive response rate of 46% vs 34% for a 2 week course of the antibiotic Rifaximin. The Rifaximin non-responders who received herbal therapy afterwards, achieved a 57% success rate with no side effects.

Triple antibiotic therapy for these harmful bacteria achieved a 60% success rate but there were side effects in some individuals including, hives, anaphylaxis, diarrhea and Clostridium difficile infection.4

Furthermore, a month's supply of Rifaximin retails for $1247.39, and according to Medicare part D, a patient's copay in 2014 will be $638.09 for preferred ($703.70, non-preferred) at your local pharmacy or mail order. If you have to use triple antibiotic therapy because the Rifaximin didn't work, your costs are going to increase substantially. The herbal protocol runs less than $300 for a supply that will last a little over a month.

In the above clinical study, patients were given either;

Biotics Research Dysbiocide and Biotics Research FC-Cidal


Candibactin AR and Candibactin BR

Unfortunately, the clinical study itself did not determine which line of products worked better than the other. Reading the customer reviews on Amazon, the Candibactin products seem to work a little better. Looking at the ingredients, I would go with the Candibactin products as well, but it is your choice.

Most of these bacteria also build biofilms that protects them from antibiotics and natural remedies. There is a very good explanation of bacterial biofilms found here. My suggestion to break through these biofilms so all of the natural antibiotics or prescription antibiotics are more effective while improving your success rate, is to take Biofase. Biofase is designed to eat through these biofilms, yeast too, and dosing directions can be found in the charts below.

You can also increase your chances of clearing these infections by using the motility agent Iberogast. Clinical studies performed by doctors Ottillinger B, Storr M, Malfertheiner P, Allescher HD at the Life Sciences Consultancy in Germany, show that without a motility agent, 60% of people treated for sibo tend to relapse.5  Follow the dosage directions on the label and take either right before or with meals, see charts.

Because many of these bacteria consume sugar for food, I would follow the candida diet or at least cut way back on the amount of sugar you consume. That includes grains, which typically have a glycemic load greater than sugar itself.

One of the other problems that could be associated with these harmful bacteria are high iron levels, especially with bacteria that build biofilms. So if your levels are high you need to take something to remove the excess iron such as lactoferrin. Lactoferrin binds iron while stimulating the immune system. The bound iron is then passed in your stool.

Severe cases or those that don't respond, will need to repeat the therapy while following the Elemental Diet. If that doesn't work and for infections in the large intestine only, a fecal matter transplant is your last alternative.

Pregnant women should consult with their doctor before following this protocol.

Suggested Directions

First Week

Biofase Take 2 capsules 1 hour before breakfast and 1 capsule 30 minutes before bedtime.
Candibactin AR Take 1 capsule twice a day right before or with breakfast and dinner.
Candibactin BR Take 2 capsules twice a day 30 minutes before breakfast and dinner.
Iberogast Take the recommended dose with meals 3 times per day.
Lactoferrin Take 1 capsule at bedtime.

Week Two and Until Products are Gone

Biofase Take 3 capsules 1 hour before breakfast and 3 capsules 30 minutes before bedtime.
Candibactin AR Take 1 capsule three time a day right before or with meals.
Candibactin BR Take 2 capsules three time a day 30 minutes before meals.
Iberogast Take the recommended dose with meals 3 times per day.
Lactoferrin Take 2 capsules at bedtime.

If you decide to use the Biotics Research products instead of the Candibactins, just follow the directions on the label in place of the Candibactin products.


If the above protocol initially causes a cleansing reaction that you can't handle due to the severity of your infection, you can always reduce doses and work up as you are able.

Alternative Harmful Bacteria Protocol

On every single stool test I have seen, there are four products that work for all of these harmful bacteria. Some of these products do work better than others depending upon species, but you are only going to know what that product is if you do the stool test. Some of these bacteria, klebsiella pneumoniae comes to mind, are susceptible to each product equally so no single product works better than any other.

However, because I quite often see follow up stool tests come back showing the original bad baceria you were trying to kill is gone, but other harmful bacteria are now out of control, I recommend you use all four.

The products are:

Tanalbit or Viracin


Oregano Oil

Uva Ursi

What I would do is take the Tanalbit everyday as directed. Take Berberine and Oregano oil 30 minutes before breakfast and dinner. Take Uva Ursi for 7 days then stop for 7 days, then repeat the cycle.

As I said in the first protocol, Biofase and Iberogast are recommended as well. Take 3 capsules of Biofase 1 hour before breakfast and at bedtime. Follow the dosing directions on the Iberogast label.

Lactoferrin would also be helpful but it is entirely up to you. If you decide to take it, take it at bedtime.

Article written by Dan and edited for accuracy by Dr. Taylor

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1. Int J Antimicrob Agents. 2011 Apr;37(4):316-23. Epub 2011 Mar 5. Combined treatment of Pseudomonas aeruginosa biofilm with lactoferrin and xylitol inhibits the ability of bacteria to respond to damage resulting from lactoferrin iron chelation

2. Pyleris E, Giamarellos-Bourboulis EJ, Tzivras D, Koussoulas V, Barbatzas C, Pimentel M. The prevalence of overgrowth by aerobic bacteria in the small intestine by small bowel culture: relationship with irritable bowel syndrome. Dig Dis Sci. 2012;57(5):1321-1329.

2. Bouhnik Y, Alain S, Attar A, et al. Bacterial populations contaminating the upper gut in patients with small intestinal bacterial overgrowth syndrome. Am J Gastroenterol. 1999;94(5):1327-1331.

4. Glob Adv Health Med. 2014 May; 3(3): 16–24. Herbal Therapy Is Equivalent to Rifaximin for the Treatment of Small Intestinal Bacterial Overgrowth

5. Wien Med Wochenschr. 2013 Feb. STW 5 (Iberogast®)--a safe and effective standard in the treatment of functional gastrointestinal disorders.
Ottillinger B1, Storr M, Malfertheiner P, Allescher HD.

Harmful Bacteria Testimonial

Hi Dan.

I had gotten rid of the yeast in the gut with high doses of grapefruit seed extract but still felt "not quite right."

I had stool samples taken and the naturopath said yeast was under control, but there was high bad bacteria count.

I searched online and found your products and tried them.

Your products helped clear up the problem.

Now I am ordering again to make sure things stay under control.

You can use this as a testimonial if you want.



How to Treat H. Pylori

I see positve results for h pylori on stool test results quite often. H Pylori is short for Helicobacter Pylori and was previously called Campylobacter Pyloridis. It is a Gram-negative, microaerophilic bacterium that literally drills its way into the stomach wall like a corkscrew.

Symptoms appear as gastritis with abdominal pain and sometimes nausea. It can also cause bloating, burping and sometimes vomiting. It can lead to stomach and small intestinal ulcers and cancer of both organs. The standard treatment is a course of broad spectrum antibiotics and acid reducing proton pump inhibitors. This is not something you really want to do if you also suffer from yeast infections, antibiotics make yeast issues worse.

My youngest daughter had this at one time and it progressed far enough that she would occasionally vomit acid and almost couldn't eat, this is what we did to get rid of it.

At the grocery store I bought the generic version of Prevacid, Lansoprazole; you only need this if you are having acid reflux symptoms. I had her take one capsule a day for two weeks. I also picked up some Mastic Gum and Tumeric and had her take one capsule of each 30 to 60 minutes before meals. About an hour after breakfast and dinner, I would have her drink a cup of tea sweetened with 1 tsp of Manuka honey and a dash of Truvia.

Within a day her pain was reduced enough where she had very few problems eating. After about a week she was back to feeling normal and no longer having any problems, except for when she took a Midol, which made her stomach bleed a little. You do have to continue this treatment for 60 days to get all the h pylori and prevent a relapse. 

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