Email :

Non-Absorbable Antibiotics for Intestinal Problems

In case of intestinal problems, the usual prescriptions are non-absorbable antibiotics, such as Rifaximin, Gentamicin, Neomycin, Vancomycin, and Nystatin. Is it a good idea? How can treatment with any kind of antibiotic be beneficial for intestinal health, when all the time we keep hearing that antibiotics have a detrimental effect on gut flora, and they should be supplemented by probiotics?

I will try to explain this below.

Small intestinal bacterial overgrowth is both a difficult to treat disease, and a complex medical problem (the topic has also been covered in this entry and this one).
So, in short, what does it entail?

Dysbiotic bacteria (ones causing adverse reaction, the opposite of symbiotic ones) ferment in the intestine and destroy the cilia. At the same time they produce toxins, which are damaging to the liver, leading to cirrhosis and fatty liver. They also have an intermediate effect on brain or mitochondria. They cause general weakening of the body, as well as memory and mood disorders.

In the case of intestinal problems, many people seek help of a doctor, hoping for the least invasive form possible: perhaps limited to a diet change, or, in the worst case, some non-synthetic agents, such as Lauricidin or Biocidin, which contain natural fungicides and bactericides.
Dysbiosis and bad bacteria

Sadly the case is not so simple. Bad bacteria are difficult to eradicate for various reasons. First, contrary to the popular opinion, they cannot be starved (although one can stop feeding them and reduce the fermentation they cause). Second, they form biofilms: colonies which are difficult to penetrate by medicines.
Additionally, the more sick the intestines, the more difficult it is to eradicate dysbiosis.

What is dysbiosis?

Many people think it is caused by a Candida fungus. While it is true to some degree, Candida itself is rarely a problem. It is often accompanied by bacteria such as Klebsiella pneumoniae (a pneumonia-causing bacillus), pathologic species of Enterococcus, the disease-causing bacillus Pseudomonas aeruginosa, Citobacter, or other species. In these cases, the bacteria need to be eradicated along with Candida.

It is a race with time – the longer the disease process lasted, the more difficult it is to treat the intestine, especially considering the increase in absorption disorders, damage to intestinal cilia, and the increasing accumulation of toxins in the body. Therefore complex and decisive actions are needed.

Treating with non-absorbable antibiotics and antifungals

Administering non-absorbable antibiotics is such an action. I wish to stress this again: non-absorbable, meaning they do not permeate the intestinal wall and act on intestinal bacteria directly.

One of the most common used is Rifaximin, its antibacterial properties being used in treating SIBO (small intestinal bacterial overgrowth). Using Rifaximin is associated with relatively minor side effects and low risk of bacteria developing a tolerance.

In a research done by Brigidi et al, it has been proven that in people suffering from ulcerative colitis, the gut flora returns to the pre-therapy state once Rifaximin is phased out. To put it in other words, it does no damage to the so-called good bacteria.

Nystatin is an antifungal, meaning it does not affect bacteria, and its effectiveness is dependent on concentration. Low concentrations of Nystatin are used to treat oral thrush, however 10x more potent concentrations are needed in order to treat fungal infection of the colon.

Gentamicin instills the most fear in patients, since it’s easy to find information on its horrible side effects, and is used even in children and infants in case of severe systemic infections. Administered intramuscularly or intravenously, it indeed can cause hearing damage. Applied orally, however, it does not absorb at all form the GI tract, even with prolonged usage. For many years it has been used in cases of hepatic encephalopathy, even for months. Hundreds of research on its absorption have been performed, all of which confirm that when administered orally it does not permeate into blood, similar to its less toxic cousin – Neomycin.

Vancomycin, similarly to Gentamicin has powerful side effects applied intravenously and does not absorb when taken orally. For many years it has been an effective weapon against Clostridum infections.

Moreover, some research shows that Vancomycin used orally may improve immunity in people. Professor Finegold used it in treatment of intestinal disorders in children with autism and has observed an improvement in cognition during the treatment.


Using the above-mentioned antibiotics, either alone or in combination, depends on the type of dysbiotic bacteria, and in the hands of an experienced doctor makes for a potent weapon against SIBO.

Antibiotic treatment should be adjusted to the strains of bacteria as closely as possible. One needs to remember about supplementing B vitamins and cleansing the intestines form leftover toxins (e.g. using Cholestyramine or GI-Detox-type natural agents). Regarding probiotics: considering the fact that probiotic bacteria can pass information regarding antibiotic resistance to disease-causing ones, they can be used after, but not during, the treatment.


Use of Oral Gentamicin, Metronidazole, and Cholestyramine in the Treatment of Severe Persistent Diarrhea in Infant
Diagnosis and pharmacological management of small intestinal bacterial overgrowth in children with intestinal failure
Oral Gentamicin Therapy in the Prevention of Neonatal Necrotizing Enterocolitis; A Controlled Double-Blind Trial
Lawrence J. Grylack, MD; John W. Scanlon, MD
J Child Neurol. 2000 Jul;15(7):429-35.
Short-term benefit from oral vancomycin treatment of regressive-onset autism.
Sandler RH1, Finegold SM, Bolte ER, Buchanan CP, Maxwell AP, Väisänen ML, Nelson MN, Wexler HM.
J Clin Gastroenterol. 2010 Sep;44(8):547-50. doi: 10.1097/MCG.0b013e3181c64c90.
A combination of rifaximin and neomycin is most effective in treating irritable bowel syndrome patients with methane on lactulose breath test.

Leave a Reply

Your email address will not be published. Required fields are marked *

three × four =

%d bloggers like this: