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.

You may also like


  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.

Leave a Reply

Your email address will not be published.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

Hello. Add your message here.