Testing & Treating Citrobacter Overgrowths

Today I wanted to share some thoughts on citrobacter. Now, this is a bacterial overgrowth that I frequently find when I test the large bowel of my patients. It is a member of the proteobacteria phylum, the enterobacteriaceae family, and it’s associated with an imbalance in the gut.

Why is citrobacter an issue?

One of the main problems with citrobacter is that when it is overgrown, it can set off, or trigger your immune system. And that is because it is a member of the proteobacteria phylum, as I mentioned, and all members of the proteobacteria phylum are made up with a substance called endotoxin in their cell walls. Endotoxins are also called lipopolysaccharide, or LPS. The research gets pretty deep and pretty complex when you dive into this but the headline here is that an overabundance of LPS rich bacteria in the gut can really set off your immune system and causes inflammation.

How did I catch citrobacter?

When we do test and citrobacter comes back elevated, the big question is, how did I catch this infection? Citrobacter isn’t so much an infection but more of an overgrowth of a bacteria that is normal and healthy in small amounts in your gut. So a better question would be how did your gut and your microbiome become so dysregulated to allow this bacteria to overgrow, when normally, a healthy ecosystem would keep it in check, and would keep it from becoming a problem.

How do we test for citrobacter?

If you go to your doctor and you run a standard stool test, it won’t detect citrobacter, they’re not looking for it. It’s not that high up there in terms of pathogens, it’s more of an overgrowth. People frequently use CDSAs or complete digestive stool analysis testing. There’s also the GI map, here in Australia we use the Complete Microbiome Mapping test. And then there’s also these whole gut microbiome tests. So in Australia, I use Microba and I love Microba, overseas I would use something like Thryve. There are a few other DNA based tests that will test for citrobacter.

Image taken from: Thryve

Natural Citrobacter treatments

So what do we do when we find a citrobacter overgrowth?

Now, most naturopaths and herbalists will try and treat it directly with herbal antimicrobials, and for me, I mean, I’m definitely going to use herbs, but I find that is kind of missing the root cause of why the citrobacter was allowed to overgrow in the first place. It is a little bit simplistic, but I always just picture a seesaw. And with citrobacter overgrowth we can see this imbalance in the microbiome, so I’m always using therapies that are going to help balance out the microbiome by feeding up those beneficial bacteria like Lactobacillus, Bifidobacteria, and then all of these bacteria that produce butyrate that no one has ever heard of. As we balance that out, citrobacter comes down.

Common interventions include prebiotics like partially hydrolyzed guar gum, galactooligosaccharides, fructooligosaccharides, probiotics as well, Lactobacillus reuteri is a really big one here, and then very targeted herbal medicines frequently rich in polyphenols.

So that’s an overview on citrobacter overgrowths. Thank you so much for watching. If you liked the video, then hit the like button or leave a comment below. And if you live in Australia and you are suffering from digestive health symptoms, maybe you’re concerned or you know that you have a citrobacter overgrowth, then consider getting in touch with me here at Byron herbalist. I’d love to hear from you. All right, we’ll see in the next video.

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  1. My 17 year old son had Blastocystis Hominis and Dientamoeba Fragilis infections in his gut and after becoming extremely unwell was treated with intercolonic antibiotics. He felt no better and now has dysbiosis. Citobacter Freudi and Streptococcus anginosus are high and L. Paracasei and L. Acidophilus and very low. He experiences pots when taking certain supplements and probiotics. His SIBO test was negative.
    He is just taking S. Boulardi L.acidophilus and L.paracasei and is tolerating them well.
    He has seen a couple of naturopaths that have not been able to help him and so is reluctant try more so is under the care of a holistic doctor. He did try phytaxil but this caused POTS (very high blood pressure) so he stopped.
    He has improved a little after being on these probiotics for a few weeks. Is there anything else you could recommend for him to do. He is gluten and dairy free as now intolerant and on a low sugar diet.

    1. Hi my name is Lisa, I am 51 I have been battling these infections for a while. I had my bladder removed in September in hopes that this nightmare would end.. 😢 No Luck. Please give me some advice on what 2 do.. Thank You!!

  2. A growing number of people are becoming intolerant to probiotics mounting an immune response to them. Would just the prebiotics you mention be a good place to start?

  3. Hi There,
    I really appreciate that there is now recognition of Citro Bacter overgrowth and the issues it causes. I was tested by a Naturapath in Ontario, Canada just before the pandemic, however the medication prescribed warned of possible kidney damage and I already have decreased kidney function, so consequently I left it alone and went back to searching for something a little safer. This also was known to kill off citro bacter and so my concern was also, that as you have said here in this article that other microbes can become disregulated as a result.

    So, my issue now is that we have since moved to New Brunswick, Canada, and I have not been able to find an NP that knows how to treat Citro Bacter. Since I have had this over growth now for many years and am down to very few foods now due to the histamine intolerance that has accompanied this I am pretty desperate to find an answer.

    If you can answer me back with any help at all it would be so appreciated. If I could just know the herbs and their dosages and frequencies of taking I will try to just purchase what I can from a Natural Nutrition Store. Really, any advise you can share with me would be great. I am a prisoner to my house as I cannot go out for long because of my diet.

    Thank you so much for all you do to help people like me.

    1. You need to upload your results to the gut club stool test discussion group on Facebook – I’ll be happy to try chyme in over there.

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