Dysbiosis & Stool Testing: Klebsiella Overgrowth Spotlight

dysbiosis Nov 19, 2020

Klebsiella pneumoniae is a gram negative bacteria that can be found normally in the gut flora. Sometimes it is elevated on a stool test which is relevant since it has been found to be associated with Rheumatoid Arthritis (RA), an autoimmune cause of joint pain and swelling.

Klebsiella overgrowth is a type of dysbiosis in the colon.

So, what are the symptoms?


Do You Have Dysbiosis? 🙄

  1. Do you get stomach bugs?
  2. Do you have chronic diarrhea or constipation?
  3. Do you notice that you have brain fog?
  4. Do you have gas, bloating and abdominal discomfort most days?
  5. Do you notice that you have intolerance to carbohydrates, especially beans and fibre? 
  6. Do you have low energy most days?
  7. Do you feel depressed or anxious?
  8. Do you have chronic sinus congestion?
  9. Do you have itching in the vagina, anus, or other mucosal membranes?
  10. Do you have chronic bad breath?


These are all clues that can help guide you towards the next steps: testing and treatment.


To kill bacteria in the gut, you would need to either:

1) Take prescription antibiotics specific to your gut condition

2) Take herbal antibacterial botanicals - this is just as effective but takes longer

3) Do the Elemental Diet for at least 2 weeks - this is a treatment specific for SIBO, which is different from dysbiosis in the colon, but can be very effective 

NOTE: If you are only using a low FODMAP diet to address your IBS, this is not killing off the bacterial overgrowth. It is giving you symptomatic relief only. It's up to you if you want to try this kind of diet, but I would suggest it only for the short term in order to avoid nutritional deficiencies. 


Like many other gram negative bacteria, Klebsiella produces endotoxins called LPS which can create a die off reaction as you start to kill the bacteria. This makes you feel worse for a few days. 

If the die-off reaction is really bad, there may be a contributing yeast/candida die-off as well. If this is the case for you, try to reduce the dose of your antimicrobial treatment or take away one or two ingredients if you can. 

Keep in mind it is also important to support your organs of elimination such as the lymphatic system and liver detox pathways, because that is where the toxic debris can get stuck.  

Klebsiella is also capable of hiding in the biofilm. This may not be addressed with the initial treatment but is an adjunct treatment to the antimicrobial protocol. 

Biofilm is a protective layer where different microorganisms hibernate, making it more difficult for the antibacterial drugs or herbs to kill it. 


Sometimes what can happen is the normal bacteria from the colon travels to the small intestines, where it shouldn't be. It has access to more food particles here and starts to ferment them, producing gases. 

This then leads to bloating and pain or discomfort in the abdomen. We call this SIBO, a common cause of IBS. There's different types of SIBO you can learn more about here. A stool test only tells us about the colon, so we can't diagnose SIBO based on this.  

If you have done a comprehensive stool analysis already, I would encourage you to check for SIBO with a breath test. These two types of investigations can be really informative for treatment and make a big difference in figuring out what is going on in your gut.

Beyond stool and breath testing, once your dysbiosis and SIBO are under control, it's time to look at the underlying cause of your gut inflammation to begin with. It may be lyme, mold toxicity or hypothyroidism to name a few. By addressing the underlying cause, you are preventing the SIBO relapses which are very common and supporting your long term health.