GI Map Test Opportunistic Bacteria and Dysbiosis

GI Map Test Opportunistic Bacteria

The GI Map test covers a lot of different areas to assess your gastrointestinal health, and the GI Map test opportunistic bacteria section is one of the most important.

People are often relieved to see that they don’t have serious pathogenic infections listed on page one of the report. However, high levels of opportunistic bacteria are a sign of dysbiosis and can cause a wide range of digestive symptoms.

Opportunistic bacteria are even considered normal in the stool at low levels, and for most people will not cause symptoms. However, high levels of these bacteria can cause diarrhea, constipation, inflammation, pain and even systemic inflammation that can cause joint pain and skin problems.

Some of these bacteria are also associated with mood and cognitive disorders.

GI Map Test Opportunistic Bacteria And Dysbiosis?

There are two main types of dysbiosis, and both can cause digestive symptoms and affect your overall health.

  1. Undergrowth dysbiosis - not enough of the beneficial bacteria, this includes Bifidobacterium, Lactobacillus, Roseburia, Akkermansia and Faecalbacterium prausnitzi
  2. Overgrowth dysbiosis - this is too much of the opportunistic bacteria and this is the type that will usually cause the most symptoms.

Overgrowth and excessive colonization by opportunistic bacteria may occur when the commensal bacteria are impaired by poor diet, antibiotic use, parasitic infection, food poisoning, high stress or a weakened immune system.

When intestinal permeability is present (see zonulin), these microbes can escape the lumen of the gut and can cause systemic infections.

For many people it is this overgrowth of opportunistic bacteria that is the main cause of their symptoms.

What Symptoms Does Dysbiosis Cause?

Many people can have mild dysbiosis without realizing it, it’s only when things get really out of balance due to diet, stress, or infections that symptoms may manifest.

Physical Symptoms of Dysbiosis

  • Aching joints
  • Acid reflux
  • Bloating
  • Constipation
  • Diarrhea
  • Reacting to foods that were previously fine
  • Excess Gas
  • Heartburn
  • Skin problems like acne, skin rashes, and psoriasis
  • Stomach pain

Gut dysbiosis can also affect your emotional/mental health

  • Anxiety
  • Brain fog
  • Depression
  • Poor memory
  • ADHD or ADD

Identifying Opportunistic Bacteria With The GI Map Test

Bacillus spp.

Bacillus spp. represents a group of gram-positive bacteria within the Firmicutes phylum, often found in the human gut. While some strains serve beneficial roles as probiotics, abnormally high levels can indicate underlying issues such as impaired digestive function, small intestinal bacterial overgrowth (SIBO), or constipation. 

Also Read: SIBO Guide(to help you eliminate IBS)
Most people should have the Bacillus species present and it is only an issue at high levels.

Enterococcus faecalis & Enterococcus faecium

Enterococcus faecalis and Enterococcus faecium are gram-positive bacteria in the Firmicutes phylum. Elevated levels in the gut may stem from low stomach acid, use of proton pump inhibitors (PPIs), or compromised digestive health, often linked with SIBO or constipation. Their natural resistance to several antibiotics can lead to overgrowth, complicating treatment strategies.

Morganella spp.

Morganella spp. belong to the Proteobacteria phylum and are notable for their ability to produce histamine. Elevated levels in the gut are often a marker of increased intestinal inflammation, which can manifest as diarrhea and may be related to conditions like SIBO. Individuals with histamine intolerance need to be particularly cautious of Morganella overgrowth.
This bacteria is a problem for people with histamine intolerance or MCAS

Pseudomonas spp. & Pseudomonas aeruginosa

Pseudomonas spp., including Pseudomonas aeruginosa, are gram-negative bacteria that can become problematic at high levels, indicating possible intestinal inflammation. This may lead to symptoms like abdominal cramps and diarrhea. Additionally, certain strains produce lipopolysaccharide (LPS) toxins, which are harmful to cellular structures and can exacerbate symptoms.

Staphylococcus spp. & Staphylococcus aureus

Staphylococcus spp., including Staphylococcus aureus, are gram-positive bacteria within the Firmicutes phylum. Elevated levels often reflect reduced digestive efficiency and increased intestinal inflammation. Toxin-producing strains of these bacteria can aggravate these issues, leading to symptoms such as diarrhea and loose stools.

Streptococcus spp.

Streptococcus spp. are gram-positive bacteria from the Firmicutes phylum that naturally colonize the skin and mucous membranes. In the gut, however, elevated levels can arise from factors like low stomach acid, prolonged PPI use, or reduced digestive functionality. These bacteria are often associated with gastrointestinal disorders such as SIBO and constipation, and high concentrations can lead to inflammation and loose stools.

Desulfovibrio spp.

A genus of Gram-negative sulfate reducing bacteria. The bacteria produce hydrogen sulfide (H2S), a metabolite which can influence cell signaling and reduce oxidative stress at low concentrations and pose toxicity at higher concentrations.
Everyone will have this present but you do not want to have high levels, are common cause of foul smelling gas


Family of bacteria-like microbes that produce methane. Facilitates carbohydrate fermentation and short-chain fatty acid production by beneficial bacteria. High levels are linked to chronic constipation, as well as some types of SIBO and IBS. Low levels may indicate reduced production of short-chain fatty acids and may be associated with inflammation.

GI Map opportunistic bacteria explained

Citrobacter spp. & Citrobacter freundii.

Citrobacter spp., including Citrobacter freundii, are gram-negative bacteria in the Proteobacteria phylum. Elevated levels may suggest heightened intestinal inflammation, often observed in conditions like small intestinal bacterial overgrowth (SIBO). Monitoring these bacteria can help in diagnosing and managing associated digestive disturbances.

Klebsiella spp. & Klebsiella pneumoniae

Klebsiella spp., including Klebsiella pneumoniae, are gram-negative bacteria that naturally inhabit the oral and respiratory tracts. High levels in the gut, especially after prolonged antibiotic use, can lead to symptoms like diarrhea, bloating, and abdominal pain. These bacteria can also release histamine, aggravating inflammation and are linked with Ankylosing Spondylitis.

Mycobacterium avium subsp. Paratuberculosis

Mycobacterium avium subsp. paratuberculosis, part of the Actinobacteria phylum, is notably associated with significant health conditions such as Crohn's disease and rheumatoid arthritis. While not commonly detected on the GI Map test, its presence at elevated levels can be a critical diagnostic marker.

Proteus spp. & Proteus mirabilis

Proteus spp., including Proteus mirabilis, are gram-negative bacteria that can signal increased intestinal inflammation when present in high amounts. These bacteria can cause symptoms like diarrhea and are often contracted from pets or wild animals, underscoring the importance of hygiene in managing gut health.

Fusobacterium spp.

Genus of gram-negative bacteria in the Fusobacteria phylum. Commonly found in the oral cavity, and may also be found in the intestine. Associated with inflammatory processes, as well as autoimmune conditions such as systemic sclerosis.
Commonly found at low levels on the GI Map test

Prevotella spp.

Gram-negative species in the Bacteroidetes phylum. Associated with rheumatoid arthritis. High levels may result from reduced digestive capacity, or a high-starch diet.
Common to see low levels and this is usually not a problem.

Opportunistic bacteria species on the GI Map test

These are the dysbiotic and autoimmune related bacteria on the GI Map test

Treatment Options For Dysbiosis

It’s important when assessing the GI Map test to not just look at each individual marker in isolation, you need to look at the test as a whole and also take into account each person’s signs and symptoms.

While supplements can help, and are often needed to get things back into a balanced state, the most important thing to focus on first is diet and lifestyle changes.


If you have an overgrowth of opportunistic bacteria a short term low FODMAP diet is often needed, this is usually for around 3-4 weeks and once symptoms such as gas, bloating and constipation/ diarrhea improve then it is time to start adding foods back into the diet.

The low FODMAP diet, or any restrictive diet should only be for as short a time as possible, this is because a wide variety of foods is important for the microbiome.

Sleep and Stress

Poor sleep leads to physical and emotional stress on the body, plus stress from work, relationships, or past trauma can also affect gut health.

Also Read: 12 Tips to Sleep Better

Many people with dysbiosis, find that their diet gets more and more limited, and this can be stressful, especially in social situations.

Mindfulness meditation and breathing exercises such as box breathing or the 4-7-8 breathing technique can be really helpful in this situation.

An excellent program to help the gut-brain connection is called Nerva, this is a self-hypnosis program to help address the nervous system. Clinical trials have shown great success with this program, and I have heard a lot of positive feedback from clients.


Treatment should be an individualized approach, and there is not one set protocol that will address the gut microbiome imbalances. Don't just rely on supplements or medications but make sure you also address diet, stress and other triggers.

I also believe that it is not a good idea to prescribe too many supplements, otherwise you don’t know what is helping, or if someone has side effects it is hard to know what is causing them.

Start with 4-5 supplements and address things in the right order. This will depend on your results but if Helicobacter pylori is present this should often be treated first, or if there is a lack of enzymes or a lot of inflammation/ low SIgA this may need to be addressed before tackling the high levels of opportunistic bacteria.

Also Read: Tips to Test and Balance SIgA

Treatment is not just about “killing” unwanted bacteria, I always recommend emphasizing improving the beneficial levels of bacteria with diet and prebiotics as part of a treatment plan.

GI Map Test Opportunistic Bacteria Summary 

The GI Map test is mainly focused on identifying problems in the large intestine, it can give clues as to whether SIBO is an issue but some people may need a specific SIBO test or another option is the Food Marble device for measuring SIBO.
*clients can schedule a consultation to get a 15% discount link for Food Marble and you will also be connected to my account so I can review your results.

I always recommend working with an experienced practitioner to help you assess the GI Map results, this can save money and time in the long run by not wasting money on ineffective supplements or not focusing on the most important things first.

Click on the link below to schedule a consultation at Planet Naturopath - all consultations are via Zoom or phone and we work with clients worldwide.

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