Have you had a GI-MAP or stool test come back showing elevated Citrobacter freundii?
You might be wondering whether this bacteria is causing your bloating, weird stools, or other digestive symptoms, and whether you need to treat it.
Citrobacter freundii is a type of bacteria that can naturally live in the digestive tract. In some circumstances, it can cause infections or become more problematic.
However, finding Citrobacter on a stool test doesn’t automatically mean you have an infection or need treatment. The important thing is to understand what your result means in the context of your symptoms and overall health.
Let’s see what an elevated result might mean, and what to do about it.
What Is Citrobacter freundii?
Citrobacter freundii is a type of bacteria that can be found in the intestines, as well as in the environment, including soil and water.
Think of your gut as an ecosystem. It contains many different types of bacteria that normally coexist without causing problems. Citrobacter can be part of this ecosystem, but it can also act as an opportunistic pathogen.
An opportunistic pathogen is a microorganism that can cause problems under certain conditions, rather than causing disease every time it is present.
For example, Citrobacter can cause infections in the urinary tract (UTI) or other parts of the body. However, its presence in a stool sample is a different situation. It does not necessarily mean the bacteria are causing an active infection or contributing to your digestive symptoms.
The important question is not simply whether Citrobacter is present, but whether the result is clinically meaningful when considered alongside your symptoms, medical history and other test findings.
What Causes Citrobacter Overgrowth?
There is no single established cause of elevated Citrobacter levels in the gut. However, several factors may influence the balance of intestinal bacteria.
These include:
Antibiotic use: Antibiotics can change the composition of the gut microbiome by affecting susceptible bacteria. They can kill “good” bacteria and leave more room for opportunistic bacteria to grow, as they tend to be more resistant to treatment.
Changes in gut motility: When intestinal movement is impaired, this can affect how bacteria and intestinal contents move through the digestive tract.
Previous gastrointestinal infections: An infection can change the gut environment and the composition of the microbiome long-term.
Underlying digestive conditions: Some gastrointestinal conditions such as SIBO can affect the intestinal environment and microbial balance.
These factors may influence the microbiome, but they have not been established as specific causes of Citrobacter overgrowth. It is also important to remember that a high result on a commercial stool test does not tell us why the bacteria are elevated.
What Symptoms Can Citrobacter Overgrowth Cause?
When people discover elevated Citrobacter on a stool test, they often want to know whether it explains their symptoms.
Possible digestive complaints include:
Bloating and excessive gas
Abdominal discomfort
Changes in bowel habits
Diarrhoea or loose stools
General digestive discomfort
However, these symptoms are not specific to Citrobacter. They can also occur with IBS, SIBO, food intolerances, constipation, celiac disease and other gastrointestinal conditions.
This is why it is important not to assume that Citrobacter is the cause of every symptom simply because it appears on a stool test.
Your practitioner should consider the overall clinical picture to be able to determine if Citrobacter is problematic or not.
Citrobacter freundii, Hydrogen SIBO and Histamine
Citrobacter freundii is relevant to gut health beyond its presence on a stool test. Let’s have a look at its link with SIBO and histamine intolerance.
Citrobacter and hydrogen production
Research has demonstrated that C. freundii can produce hydrogen gas when fermenting carbohydrates. Hydrogen is one of the gases measured during SIBO breath testing, which detects gas produced by intestinal microbes as they ferment a test substrate (glucose or lactulose).
This raises an interesting question about whether Citrobacter could contribute to intestinal hydrogen production as seen in SIBO.
However, finding Citrobacter on a stool test does not establish that it is present in excess in the small intestine or responsible for a positive hydrogen breath test. People often confuse these two points, which is why I will repeat it again: you cannot diagnose SIBO from a stool test. For a proper SIBO result, a breath test is the norm.
Citrobacter and histamine production
Some strains of C. freundii have also demonstrated the ability to produce histamine. Histamine is a compound involved in immune signalling and other bodily functions, and certain intestinal bacteria can contribute to histamine production. (See: Decoding Histamine: Triggers, Histamine Intolerance & Solutions)
If you suspect histamine intolerance and have an elevated Citrobacter marker, it could be part of the picture.
What Does High Citrobacter on a GI-MAP Mean?
The GI-MAP uses quantitative PCR, a method that detects and measures genetic material from microorganisms in a stool sample.
If Citrobacter freundii appears above the laboratory’s reference range, it means the test detected a level of bacterial genetic material above that range.
Commercial microbiome tests can provide information about the microorganisms detected in a stool sample, but their clinical interpretation has limitations. This does not mean the result is irrelevant. However, it needs to be properly interpreted by a trained practitioner rather than treated as a diagnosis on its own. I offer Lab Reviews exactly for this purpose, looking at your test reports, symptoms, and health history. I then give you my analysis and an action plan on what to do next.
How Is Citrobacter Overgrowth Treated?
Treatment depends on the clinical situation.
A confirmed Citrobacter infection is different from an elevated result on a commercial stool test. When a genuine infection is present, medical treatment may be necessary. Citrobacter freundii can develop resistance to certain antibiotics, so antibiotic selection should be guided by appropriate clinical assessment and susceptibility testing.
For people with persistent digestive symptoms and an elevated stool test result, the first step is to determine whether the finding is likely to be clinically relevant.
If antimicrobial treatment is considered appropriate, some practitioners may explore herbal antimicrobials as part of an individualised gut health protocol.
Antimicrobial Herbs for Citrobacter
Several herbs and plant compounds have demonstrated antibacterial activity in laboratory studies. Some are also used in clinical practice as part of broader protocols for digestive issues and suspected bacterial imbalances (dysbiosis).
The herbs discussed below should be viewed as potential components of an individualised protocol, not proven treatments for Citrobacter.
1. Oregano
Oregano is one of the best-known herbs used in antimicrobial protocols for digestive health.
Oregano oil contains compounds such as carvacrol and thymol, which have demonstrated antibacterial activity in laboratory research. These compounds can affect bacterial cell membranes and interfere with normal bacterial function.
Because of these properties, oregano oil is sometimes included in practitioner-guided protocols for suspected bacterial overgrowth or other digestive concerns.
Oregano oil can also irritate the gastrointestinal tract and may cause nausea, abdominal discomfort or other adverse effects. I only recommend use A.D.P. by Biotics for antimicrobial protocols.
2. Berberine-Containing Herbs
Berberine is a plant compound found in herbs such as barberry, goldenseal and Oregon grape.
It has been studied for a range of biological effects, including antimicrobial activity. In laboratory research, berberine has shown activity against various bacteria, although results can differ between organisms and bacterial strains.
Berberine is not appropriate for everyone. It can cause gastrointestinal side effects and interact with medications. It should generally be avoided during pregnancy and breastfeeding, and extra caution is needed in people taking prescription medications.
3. Garlic and Allicin
Garlic contains sulphur-containing compounds, including allicin, which forms when fresh garlic is crushed or chopped.
Allicin has demonstrated antibacterial activity in laboratory studies. Researchers have investigated its effects against different bacterial species, including organisms associated with infections.
Garlic-derived compounds are therefore of interest when studying potential plant-based antimicrobial agents.
However, the amount and activity of allicin can vary considerably depending on how garlic is prepared and how a supplement is manufactured. I often use the brands Allimax Pro or Allimed, which both contain Allisure® AC-23. You can get this product here in the US and here in Canada.
Whole garlic can also trigger digestive symptoms in some people, particularly those who are sensitive to fructans, a type of fermentable carbohydrate (Fodmap). This is why I usually recommend to use standardized allicin versus supplements that contain the whole bulb.
4. Other Herbal Antimicrobials
Other herbs and plant compounds are sometimes included in broader antimicrobial protocols, depending on the clinical picture.
Examples include:
Thyme: Contains compounds such as thymol that have been studied for antibacterial activity.
Neem: Used in traditional medicine and investigated for several biological effects, including potential antimicrobial properties.
The challenge is that evidence varies between herbs, formulations and bacterial species. A product that demonstrates activity against one organism in a laboratory may not have the same effect against Citrobacter in vivo.
For these reasons, I would highly recommend to work with a practitioner to build your protocol.
What About Probiotics?
Probiotics are another option people often ask about after receiving an abnormal stool test.
Certain probiotic strains may help inhibit Citrobacter freundii by competing with other bacteria and producing antimicrobial compounds. One of the most interesting candidates is Lactobacillus plantarum, as specific strains have demonstrated inhibitory activity against C. freundii in laboratory studies.
A small human study also found that a multispecies probiotic containing L. plantarum, L. salivarius, L. casei, L. acidophilus, Bifidobacterium animalis subsp. lactis and Bifidobacterium bifidum was associated with reduced Citrobacter abundance after 60 days of supplementation.
Lactobacillus rhamnosus may also be worth investigating, although the relevant evidence comes from animal research involving a different Citrobacter species.
What Should You Do If Your GI-MAP Shows Elevated Citrobacter?
If your stool test shows elevated Citrobacter, here are some practical steps to consider.
1. Look at your symptoms.
Are you experiencing persistent bloating, diarrhoea, abdominal pain or changes in bowel habits? Or was the result an unexpected finding when you otherwise feel well?
Your symptoms help determine what should be investigated next.
2. Review the rest of your test results.
A single bacterial marker rarely tells the whole story. Other findings may help guide further investigation, but they also need to be interpreted in context.
3. Consider other explanations for your symptoms.
Bloating, constipation, diarrhea and abdominal discomfort can have many causes. Depending on your symptoms, further assessment may be more useful than immediately starting an antimicrobial protocol.
4. Discuss treatment options with a qualified practitioner.
If antimicrobial herbs are being considered, review their potential benefits, limitations, side effects and interactions. The decision should not be based on the laboratory result alone.
5. Seek medical assessment when needed.
Severe or persistent abdominal pain, blood in the stool, unexplained weight loss, fever or signs of dehydration warrant medical assessment.
Making Sense of Your Citrobacter Results
Citrobacter freundii is a type of bacteria that can naturally live in the digestive tract. In certain circumstances, it can overgrow or even cause infections, but an elevated result on a GI-MAP does not automatically mean it is responsible for your digestive symptoms or needs to be treated.
Oregano, berberine and allicin have demonstrated antibacterial activity but their use requires evaluation and caution. The most useful approach is to interpret the result alongside your symptoms, health history and other relevant findings. If treatment is appropriate, antimicrobial herbs may be one consideration within a broader, individualised plan.
At Gut Talk, I help people investigate persistent digestive symptoms, including bloating, constipation and suspected SIBO, using an individualised approach.