The Microbes of SIBO

A popular health advocate proposed that all SIBO is caused by Streptococcus. If I understand his point correctly, it is not just that the bacteria overgrown in the small intestine, but it is also that Streptococcus infecting the “body system” and in particular the liver caused the overgrowth.

There is a small kernel of truth to this theory, but for the most part, SIBO is way more complex than a simple Streptococcus infection. You can read this post to learn about the basics of SIBO and you can read this post to learn about the real root causes of SIBO.

SIBO Microbes

Research studies have been conducted where they take a sample and culture it to identify the microbes present. Here is what they found:

  • Escherichia coli

  • Lactobacillus species

  • Klebsiella pneumoniae

  • Enterococcus species

  • Streptococcous species

  • Staphylococcus species

  • Micrococcus species

  • Bacteriodes species

  • Clostridium species

  • Veillonella species

  • Fusobacterium species

  • Proteus mirabilis

As you can see, Streptococcus is just one of many microbes that may be present in SIBO. Now, since the authors cultured instead of doing a DNA analysis, there may be additional microbes that are common in SIBO.

In addition to these microbes, the archaeon (different than bacteria) Methanobrevibacter smithii can also cause SIBO. This microbe produces methane gas and is more associated with symptoms of constipation. Yeast, such as Candida species, can also be present in the small intestine. One study found that up to 26% of people with symptoms of belching, gas, bloating, nausea, and diarrhea had a small intestine fungal overgrowth (SIFO).

How do I determine what microbes I have?

The current standard for SIBO testing is a lactulose breath test. You drink a lactulose solution and take breath samples to measure the amount of hydrogen or methane gas produced. These gases are produced when bacteria ferment lactulose. So if you show elevated amounts of these gases before a certain time point, this indicates the presence of bacteria in the small intestine.

This method does not tell you what bacteria are present. To do that, you would need to collect a sample from your small intestine. This is done in research, but not in clinical practice, as it is a more invasive procedure.

So at this point in time, standard testing only tells you if you have hydrogen-dominant SIBO, methane-dominant SIBO or mixed. We can also infer a hydrogen sulfide-dominant SIBO based on the gas pattern, but that is not always accurate. Also, the breath test has no way to reveal a fungal overgrowth (SIFO).

Sometimes, a DNA based stool analysis, such as the GI-MAP, can provide more clues to what may be going on in the small intestine. For example, if there is a Klebsiella pneumoniae overgrowth in the large intestine in the presence of SIBO, then chances are the bacterium overgrowing the small intestine is Klebsiella pneumoniae. However, since the current treatment protocol is based on what gas is present, we do not need to know what bacteria are present to treat your SIBO. This is especially true for conventional medicine, which treats all SIBO with the antibiotic rifaximin. If methane is present, some doctors may add neomycin, but typically rifaxmin is all that is used. Herbal antimicrobial therapy offers more opportunity to customize an antimicrobial protocol based on symptoms and gases present.


  • 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;94:1327–1331

  • Bures J, Cyrany J, Kohoutova D, et al. Small intestinal bacterial overgrowth syndrome. World J Gastroenterol. 2010;16(24):2978-90.

  • SS, E. (2019). Small intestinal fungal overgrowth. - PubMed - NCBI. [online] Available at: [Accessed 21 Feb. 2019].

  • Beauchamp, R.O., J.S. Bus, J.A. Popp, C.J. Boreiko, D.A. Andjelkovich, and P. Leber. 1984. “A critical review of the literature on hydrogen sulfide toxicity.” Critical Reviews in Toxicology 13 (1): 25-97

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I'm Dr. Carly and my mission is to create a health revolution. I believe that another prescription is not the answer. I believe in using natural therapies that go beyond the symptoms. And I believe that doctors should spend way more than 7 minutes with a patient.