Citrobacter Infection – Gut Health & Imbalances

citrobacter infection citrobacter infections byron bay herbalist naturopathic treatments for gut infections bacterial infections gut health and disease

Citrobacter is a common bacterial infection. It is often seen when functional gut testing is done to get to the bottom of your digestive symptoms. This article will cover how and why Citrobacter infections may be contributing to your poor digestive health and will point you in the direction of natural treatment options for this particular bacterial overgrowth. 

Citrobacter infection 

First off let’s outline some key concepts.

Citrobacter species, including the notable Citrobacter freundii, is generally regarded as being a commensal bacteria found in a healthy human gut. It only becomes a ‘problem’ when it is given the space and nutrients to grow (1).

In straight talk – Citrobacter is a bacterium that is a normal part of our gut flora. When given space to grow it can become a problem. 

Citrobacter is a member of the Proteobacteria phylum and maybe more importantly the Enterobacteriaceae family. We have covered this family in depth in a previous article that I will be pointing you to a number of times in this article. If you haven’t read it yet, maybe this is a good time to hop over there and catch up to speed – How to treat bacterial infections: A holistic approach.

While the Proteobacteria phylum is represented in a healthy gut it all comes down to numbers. When allowed to grow the members of this grouping of bacteria can cause a range of issues as seen in the image below. A classic example of dysbiosis – or an imbalanced gut microbiota. 

citrobacter infections byron bay herbalist naturopathic treatments for gut infections bacterial infections gut health and disease
Image taken from: Why related bacterial species bloom simultaneously in the gut: principles underlying the ‘Like will to like’ concept

Other members of the Enterobacteriaceae family of bacteria include 

  • Escherichia coli
  • Shigella
  • Klebsiella 
  • Yersinia
  • Salmonella
  • Enterobacter
  • Hafnia
  • Morganella
  • Proteus

The headline from the family of bacteria that Citrobacter falls into is their negative impact on the immune system.

Let me explain.

Gram negative bacteria have a product known as lipopolysaccharide found in their cell wall. Lipopolysaccharide, also known as LPS or endotoxin, is released when the bacterial cell is disrupted. This in turn sets off an immune reaction and the inflammatory cascade associated with all of those nasty digestive symptoms that you may be experiencing (2).

citrobacter infections byron bay herbalist naturopathic treatments for gut infections bacterial infections gut health and disease gut health specialist
Image taken from: Enterobacteriaceae showing the makeup of Enterobacteriaceae cell walls.  

Symptoms of Citrobacter infection

Citrobacter doesn’t always play nice. It has been associated with a whole range of different disease states throughout the body, and while these are less common, it is worth knowing.

These include 

  • Urinary tract infections (more commonly associated with E. coli
  • Respiratory tract infections
  • Central nervous system infections
  • Infectious arthritis 
  • Sepsis (bloodstream infections). 

While these complications from a Citrobacter infection are very rare in healthy adults they are more common in immunocompromised individuals and in infants (3).

In immunocompetent adults (here the immune system is functioning properly) Citrobacter infections generally stay within the gut – either the small bowel or the large bowel. I like to look at this presentation as more of a bacterial overgrowth.

While Citrobacter can play a role in small intestinal bacterial overgrowth (4), you won’t be able to determine this with the stool testing listed below. Here you will need to rely on SIBO breath testing.

Stool tests will help to determine if you have a Citrobacter infection in the large bowel. 

So which stool tests are best?

How Do I Test For a Citrobacter Infection and Overgrowth?

Due to the fact that you are reading this article I am assuming that you have already tested and found a Citrobacter infection.

Maybe you ran the comprehensive GI MAP (also known as Complete Microbiome Mapping here in Australia) as seen in the image below.

gi map australia order your gi map here citrobacter infections byron bay herbalist naturopathic treatments for gut infections bacterial infections gut health and disease
GI MAP (Complete microbiome mapping) showing no Citrobacter overgrowths. <dl equates to below detectable levels. 

A second way to test for Citrobacter infections would be another DNA based stool test that gives you a more complete snapshot of the large bowel gut biome. These include Ubiome and Microba. Here you may have to dig a bit deeper into the results and possibly even download the raw data to see if you have a Citrobacter overgrowth. This is why it is important to work with a gut savvy clinician. In the long run it saves time and money.

Another stool test that may shown a Citrobacter infection is the comprehensive digestive stool analysis (CDSA for short). These culture and microscopy tests are far less reliable and are considered outdated technology by many digestive health experts. There are so many reasons why this is the case. 

  • Number one your stool sample is shipped to the lab, which may take days to weeks. The temperature variation could lead to shifts in the microbial population in the sample.
  • Secondly the lab technicians actually have to grow the culture out. Here they use culture specific media that the bacteria enjoy growing on. Talk about skewed results!
  • Finally most CDSAs give you a rating indicating the extent of the bacteria’s growth. Unlike the GI MAP (seen above) this is completely subjective. What is the difference between + and +++? Who knows! And how does this factor into you and your possible bacterial overgrowth? 
test for citrobacter infections byron bay australia gut infections bacterial infections gut microbiome health and disease
CDSA showing no detected growth for Citrobacter and ++++ for a Klebsiella infection

Ok, enough culture and microscopy (CDSA) bashing. Let’s move on to how you may have contracted this particular infection. 

Causes of Citrobacter infections

So we have established that Citrobacter is a normal inhabitant of a healthy gut. It only becomes a problem when it is allowed to overgrow and becomes a proper bacterial overgrowth in the large bowel. But how does this process actually happen?

The ongoing debate…

Here are a few theories backed up by science.


Some researchers point to inflammation driving the overgrowth of the family of bacteria that Citrobacter falls into. They postulate that, in the presence of inflammation, less friendly facultative anaerobic bacteria (such as Citrobacter) have a competitive advantage over the obligate anaerobic bacteria (most of the beneficial bugs) in the large bowel (5).

citrobacter infections how citrobacter infections grow in your gut
Image taken from: Why related bacterial species bloom simultaneously in the gut: principles underlying the ‘Like will to like’ concept

Seeing that an expansion of the members from Proteobacteria phylum (seen in the image above) such as Citrobacter leads to systemic inflammation this quickly turns into a vicious cycle. Inflammation feeds the growth of Citrobacter which then feeds inflammation…

Lost Bacterial Balance

As with most things in nature it all comes down to balance. 

When some of the superstars of the gut have been compromised, or even lost, then this opens up a niche for less friendly bugs to move in. 

You all know the major insults to your gut flora but let’s cover them just to be thorough.

  1. Antibiotics – We all know that antibiotics can really mess up our guts. Some of you may even have first hand experience with this. The real microbiome nerds out there may have even sampled their gut microbiome and seen low bacterial diversity (a major player in health and disease). To save us covering the same subject ad nauseum I will point you here for a deeper dive into the issues surrounding antibiotic use and how they actually lead to dysbiosis and bacterial infections! Funny that…antibiotics, often used to combat bacterial infections cause bacterial overgrowths that then lead to bacterial infections. 
  2. Caesarean birth – When babies are vaginally born they inherit their microbiome from their mother. This passing of beneficial microbes from mother to child has been happening for much of our evolution. When c-sections are born they inherit much of their gut microbiome from the skin of their mother. The microbes involved in this bacterial hand-off are completely different and may contribute to an imbalanced gut.
  3. Baby formula – Formula fed infants miss out on so much goodness so much so that one scientific paper went on record saying that ‘breast milk is the perfect nutrition for infants, a result of millions of years of evolution.’ The same paper noted that mother’s milk contains prebiotics known as human milk oligosaccharides, perfect for feeding up beneficial bacteria in the newborn. 

Treating Citrobacter Infections 

A doctor will tell you to take antibiotics.

A naturopath, functional medicine practitioner or holistic doctor might tell you to take grapefruit seed extract or oregano oil.

Many times this kill focused approach may clear up your bacterial infection in the short term. In the long term this approach may leave you with a disrupted gut microbiome aka dysbiosis – the very thing you were given these heavy hitting treatments in the first place.  

This may seem confusing and contradictory. How can a treatment that disrupts or damages your microbiota make you feel better?

It is complicated.

Again we circle back to the idea of balance vs imbalance. Bacterial overgrowths represent an imbalance in the gut flora. Treating these imbalances with extremely strong antibiotic-like antimicrobial herbs (oregano oil, grapefruit seed extract, high dose berberine long term) may kill off or reduce the bacterial overgrowths. Simultaneously, it may also negatively impact the beneficial gut flora that help to maintain the balance in your gut.

This concept was presented in a paper from a microbiome researcher Martin J. Blaser as the disappearing microbiota hypothesis. As our indigenous gut flora diminish over generations different diseases become more common. As we continue to loose our ancestral gut microbes allergies and metabolic diseases are becoming more common. Are they connected? Possibly.

The graph below outlines the loss of our ancestral microbiota over the past 80 years.

Graph taken from: What are the consequences of the disappearing human microbiota?

A more considered approach would be to look at the whole gut composition. The more that I have studied the gut microbiome the more that I look at it as a complex and fragile ecosystem. This ecosystem can be modulating by selectively feeding beneficial microbes with prebiotics and very select and targeted probiotics.

Many times this will help to reduce bacterial overgrowths such as Citrobacter to healthy levels in the gut.

If digestive symptoms don’t improve then certain herbal antimicrobials may be indicated. Here we can start with herbs that are less damaging to the beneficial bacteria in our gut and move towards stronger herbs as needed. 

A microbiota centric approach

As always it takes a skilled gut clinician to assess and determine which course is best for you and your digestive symptoms. 

Take it from me. 

It took me five years plus to treat my gut imbalances. I was learning as I went and spent more money and time than I should have as I tried to get to the bottom of my digestive issues. In the end it took working with a gut savvy clinician to really help shift the needle. 

From this journey I have been piecing together the best (and least harmful) approach to treating gut infections such as Blastocystis hominis (which may or may not need to be treated in each specific case), bacterial overgrowths in the small intestine and the large intestine

If you would like to work with me please head over here to book an initial 60 minute appointment.

As always please feel free to leave a comment and share your thoughts on your experiences with digestive health, prebiotics, probiotics and herbal medicine in the comment section below.

References and Resources

  1. The clonal relationship among the Citrobacter freundii isolated from the main hospital in Kermanshah, west of Iran
  2. Infections due to Citrobacter and Enterobacter 
  3. Citrobacter Species
  4. Small intestinal bacterial overgrowth is associated with irritable bowel syndrome and is independent of proton pump inhibitor usage
  5. Why related bacterial species bloom simultaneously in the gut: principles underlying the ‘Like will to like’ concept
  6. Mother’s Milk: A Purposeful Contribution to the Development of the Infant Microbiota and Immunity.
  7. What are the consequences of the disappearing human microbiota?
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  1. Hello Tod,
    I am Anira from Hungary.
    I have SIBo and dysbiosis. I habe Citrobacter owergrowth. I do not know how to kill this bacteria but do not harm good bacteris which I do not have many. Could you tell me which herbs to use?
    Thank you

  2. I have citrobacter does it also affect the bladder kidneys urethra skin scalp and how do I rid of it without antibiotics am very sensitive to herbs I’ve been on many antibiotics and Also tapering Ativan and just moved out of mold am on amoxicillin now for uti and also have bacterial vaginitis that I can’t rid of my face scalp skin urethra burning body bloat bad in gut and Diarhea or constipstion bladder burns I have high histamine I’ve heard n longum bb536 can help eradicate this csn this bacteria cause high histamine in the body head to toe

    1. I have had citrobacter for a few years thet keep giving me herbs and antibiotics and I Cant clear it can you help

      1. Shifting the pH of the large bowel is usually quite effective at clearing or significantly reducing citrobacter. Probiotics, prebiotics or even good quality butyrate may be indicated depending on the case.

  3. I had a MARCoNS swab that showed:
    Entercocco SPS
    Staph Aureus COAG POS
    Citrobacter Freundii

    I was diagnosed with MRSA in my nares over 5 years ago. I am sure its still there. PND, itching, burning, hurts. Do you deal with those?

  4. Are you still doing 15 minute consultations to determine good fit? Long-standing Citrobacter F or B infection (showed up as each, respectively on GI stool tests-not sure if that is just a result of renaming-categorization of Citrobacter species. anyhow, I have treated it with Rifaximin three times, GFSE, Oil of Oregano, Uva Ursi, Caprylic acid, berberine, plant tannins, etc. I now have enthesitis (joint insertion inflammation) d/t chronic inflammation? I’m fed up. Can you help? I’m in boulder CO. I’m 47, female.

    1. I have read that MRSA is treated (esp in Australia, even in hospitals) with raw Manuka honey. This is available at most health stores in US. Did not find info on whether they use it topically or ingested or both. Can’t hurt to try it, but use a good dosage (Tblsp), twice a day for at least a week. It’s pricey, but effective.

  5. Hi Todd, Just been diagnosed with Citrobacter, caused UTI Been prescribed antibiotics. Very reluctant to take them. Can you recommend treatment. Or point me in the right direction.
    London… Thank you

  6. I used bacteriophages from Georgia to eradicate citrobacter from my gut, and I had significant improvement. Antibiotics and herbal antimicrobials didn’t work. I tried for years.

    The modern infections are basically superbugs and are just too strong. We need innovation in treatment.

    1. Hi Robert, I’m interested to find out why you decided to go for bacteriophages? How does it work? What were your symptoms before?

      1. Hi Robert,

        I am happy to hear that the bacteriophages worked for you. I have suffered for years with Citrobachter. Could you please forward me some info on the place in Georgia. Thank you in advance!

  7. Hi, I suffer from histamine Intolerance that clearly has a direct correlation from citrobacter infection in my gut. I’ve been taking the holistic approach with supplements for the last 1.5 years. I’ve been on low histamine diet for 2 years. I just had my 1.5 year follow up & found that the Kleisabella infection has cleared, but I still have SIBO & Citrobacter present. My functional med doc has prescribed xifaxin antibiotic to help clear these two so, maybe I can lead a normal life without anaphylaxis. What are your thoughts on 1 round of this to help clear it? I haven’t taken antibiotics in 15-20 years. I am not immune compromised & I rarely get sick.

  8. Hi, I had a diagnosis of Citrobacter Freudian complex. Most of my beneficial flora is excellent except Enterococcus spp and Lactobacillus support a little low. The Citrobacter fr frundi showed that it would respond to Uva Ursi extremely well. My Dr said I could choose that or ciprofloxin. I chose the natural route but he did not tell me how much, dosage or length of time. Also what form is best.

  9. Hi
    I have had citrobacter Freundi for weeks and now have citrobacter youngee. 2 months of antibiotics and cephalosporins have not killed it at all. I am immune compromised and 69 yrs
    old. Any ideas to help my gut please?

    1. Hi Terrie, I haven’t found antibiotics to be so helpful with citrobacter and the enterobacteriaceae family in general. Most seem pretty darn antibiotic resistant. Shifting the gut pH with probiotics and prebiotics can work wonders in most and targeted herbal antimicrobials are generally very helpful.

    2. I have citrobacter Freudii and Cocksackie.
      I’ve been advised to take UVA Ursi for 12 days only.
      Do you know what I can take for Coxsackie virus?
      Would these cause continuous severe palpitations?

  10. Is there specific diet for overgrowth of citrobacter and can citrobacter cause sibo I have overgrowth of citrobacter I was put on ceurofixime and a probiotic 100 billion

    1. Hi Teresa,
      It is noted that Citro Bacter overgrowth leads to histamine intolerance, therefore if you research low histamine foods this should give you some idea. The other interesting thing I discovered last summer from a friend is that “left overs” grow exponentially in histamine and therefore, it is recommended for people with histamine intolerance to eat only fresh foods and frozen foods. I make my own homemade soup for lunch once a month, and put it in
      serving sized jars with lids and put them directly into the freezer once cooled of course. These are then taken out daily and defrosted just before use. I also cook my chicken for the week and freeze it in breast portions in baggies once cooled and once again pop one out and defrost it right before I’m going to eat it. I did find this helped with my histamine response symptoms however give it time. I think I didn’t really see a difference until about the third week in. Hope this helps. I have yet to find a NP that deals with Citro Bacter and therefore any help you get would be appreciated if passed on to me. Hope this helps you in your journey to health.

  11. Hi Todd, do you ever use Uva Ursi for Citrobacter Freundii in the gut? On my stool test testing, it show Uva Ursi to be highly effective on the bacteria but all my googling and reading really only points to that for UTIs, which I do not have.

    I’ve also read a lot about how prebiotics feed Citrobacter Freundii (especially FOS). Do you find that to be true?

    Would love to work with you but I’m based in the US. Thanks so much if you’re able to reply.

    1. Hi Nikki, Thanks for your comment. I use uva ursi frequently for enterobacteriaceae family (citrobacter is in here) and get good results. I’m not concerned around FOS feeding this family either but rarely use it. It can be highly reactive in my sensitive patient population. PHGG almost every time!

  12. Hi Todd, I haven’t seen anyone talk about citrobacter koseri high (doctor data’s stool test). I read that in rare cases it can cause meningitis with symptoms of headaches, confusion and photophobia, all of which I have. Plus I just suffered a TGA when I started Xifaxin, wondering if there is a connection. I’ve stayed on the xifaxin for sibo, which I’m not convinced I have since doctor didn’t do the traditional testing but said from stool test it was sibo. Stomach is severely distended but no other symptoms in GI., just severe brain fog and memory problems all exacerbated by xifaxin. Memory issues are scary. Thanks.

  13. Hi Todd, I was diagnosed with Citrobacter koseri in my urinary tract, antibiotics do not help. Is there a way to get rid of this using natural remedies?

  14. Hello Todd. After a long treatment with clindamycin, due to a dental problem, I got Clostridium difficile, so I was treated again with an antibiotic called vancomycin. After a long recovery process that has not yet ended, I found out that I carry Helicobacter pylori and the doctor wants to treat me again with three types of antibiotics. I feel that I will not be able to withstand this treatment. I felt it could kill me. Is there a treatment that is not based on antibiotics for Helicobacter pylori? Thanks for any assistance.

  15. Hi Todd, hope all is well since you have not responded to the last few post on here from people. I wanted to get your thoughts on growth of Citrobacter Koseri found in the nasal passages. Does that also have to do with gut health?

  16. Hi Todd. Thank you for a great article and all the info you provide. I did treat my high Citrobacter spp w oregano oil. Since I have high staph and strep bacteria too, combined w low elastase I’ve made efforts to increase acidity in my gut (I also have h pylori). I’ve been using betaine and pepsin w meals but also drinking lemon water on an empty stomach first thing every morning. I use juice of a whole lemon. This is also supposed to be super healthy for the liver. However, I have recently read that Citrobacter feeds on citrine. Is this true? Should I be avoiding lemon water unless I’ve completely eradicated the Citrobacter spp? You also mentioned changing PH can help w a citribacter overgrowth – did that mean increasing acidity?

    1. hey cathy, thanks for the input. I wouldn’t be so concerned with the lemon and a citrobacter overgrowth for most of my patients. Acidify you large bowel by improving/increasing short chain fatty acids, mainly butyrate. Lately I’ve been using more direct butyrate supplementation with great results in the right patient too!
      Hope that helps!

  17. I’ve just been diagnosed with uti and the urine test shows Citrobacter Braakii abnormal, doctor put me on doxycycline is there anything I can do to rid myself of this infection. I’ve had ischemic colitis and gastritis a few months ago and now this. Any help would be appreciated. I live in Las Vegas do you know any specialist here.

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