To Book an appointment at one of our UK IBS clinics in London, Brighton, telephone or Skype  please call 01273 775480 or email [email protected]


To Book an appointment at one of our UK IBS clinics in London, Brighton, telephone or Skype  please call 01273 775480 or email [email protected]

Gastrointestinal function is critical for good health. In addition to performing digestive functions, the intestinal tract contains significant amounts of organisms. Imbalances in this internal ecosystem and the overall GI function is associated with a wide variety of common illnesses including, but not limited to:

  • Irritable Bowel Syndrome (IBS)
  • Inflammatory Bowel Disease (IBD)
  • Diabetes
  • Obesity
  • Cardiovascular Disease
  • Celiac and Other Malabsorption Disorders
  • Mood Disorders
  • Autoimmune
  • Autism

There are a number of different reasons why our gut health can be compromised such as pathogens, parasites, low digestive secretions, infection, and inflammation or compromised beneficial gut bacteria.  All of which are measured in the GIMAP Stool Profile.

About this test

The Gastrointestinal Microbial Assay Plus (GI-MAP) is a comprehensive clinical tool that measures the gastrointestinal microbiome from a single stool sample using quantitative polymerase chain reaction (qPCR) technology.

The GI-MAP is designed to assess a patient’s microbiome with particular attention to microbes that cause disease or that disrupt normal microbial balance and contribute to perturbations in the GI flora and contribute to illness. With full PCR quantification, we can now see the level of infection thus, providing accurate, actionable clinical information. The results gleaned from this digestive profile help the clinician to provide personalised, targeted protocols to address gut dysfunction.

Additionally, the quantification of the levels of identified bacteria offers a useful ability to see how treatments are working because a retest can show whether a parasite has resolved, dysbiosis has improved, and more.

1. Pathogens

The GI-MAP includes pathogens (bacterial, parasitic, and viral) commonly known to cause gastrointestinal infections. However the presence of a pathogen may not necessarily result in the presence of symptoms. Many factors, including the health of the individual, the transient nature of some pathogens, and the severity of the presence and expression of the pathogen can all influence whether symptoms will express and persist.


  • Campylobacter
  • difficile Toxin A
  • difficile Toxin B
  • Enterohemorrhagic coli
  • coli O157
  • Enteroinvasive coli/Shigella
  • Enterotoxigenic coli LT/ST
  • Shiga-like Toxin coli stx1
  • Shiga-like Toxin coli stx2
  • Salmonella
  • Vibro cholerae
  • Yersinia enterocolitica


  • Cryptosporidium
  • Entamoeba histolytica
  • Giardia


  • Adrenovirus 40/41
  • Norovirus GI
  • Norovirus GII

2. Helicobacter Pylori

Studies show that nearly 50% of the world’s population may carry H. pylori. Many carriers show no symptoms at all, however, H. pylori is known to have a causative role in ulcers, chronic gastritis, and stomach cancer.

Additionally, in early phases of colonisation, patients may experience low stomach acid or hypochlorhydria. Over time, additional H. pylori strains may colonise, including those with Virulence Factors making the bacteria more harmful and increased disease potential.

Virulence Factors reported:

  • Virulence Factor, babA
  • Virulence Factor, cabA
  • Virulence Factor, cabPAI
  • Virulence Factor, dupA
  • Virulence Factor, iceA
  • Virulence Factor, opiA
  • Virulence Factor, vacA

3. Normal / Commensal / Beneficial Bacteria

Trillions of microorganisms inhabit the human intestine to make up a complex ecosystem that plays an important role in human health. The gut microbiota is diverse, varies among individuals, and can change over time, especially during developmental and life stages and with disease. The microbiome is viewed as an integral part of the body. Research has demonstrated the bacteria in the gut interact with the immune system and play an important part in immunity.

The individual species in these gut communities were long considered commensal organisms, meaning they were neither pathogenic nor particularly harmful when in their natural site and in a proper amount – in balance.

The predominant classes or families of bacteria in the gut are Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria.

Some of the jobs gut bacteria do are;

  • Producing short-chain fatty acids (SCFAs)
  • Helping digestion
  • influencing the immune system
  • Modulating GI hormone production
  • Maintaining gut barrier function and motility
  • Modulating oxidative responses
  • Producing vitamins (e.g. biotin, vitamin K)
  • Metabolising xenobiotics and phytochemicals – removing toxins
  • Preventing colonisation by potential pathogens

Optimal healthy gut microbiota – bacterial balance and composition is different for everyone. The composition of each person’s microbiome is highly variable and can change according to age, ethnicity, location, diet, lifestyle, medications, and environmental factors.  Rather than concentrating on any one commensal bacteria, understanding overall patterns
is essential when assessing the impact of individual results.


  • Akkermansia Mucinophilia
  • Bacteroides fragilis
  • Bifidobacterium
  • Clostridia (class)
  • Enterobacter
  • Enterococcus
  • Escherichia
  • Faecalbacterium prausnitzii
  • Lactobacillus spp


  • Bacteroidetes
  • Firmicutes
  • Firmicutes/Bacteroidetes Ratio


Many bacteria measured on the GI-MAP are considered opportunistic pathogens since they may only cause symptoms in some individuals, particularly those with compromised immune systems. Many people come into contact with these opportunistic bacteria species  and experience no symptoms at all. They can be considered to be a normal part of our microbiome, however, for vulnerable patients they can cause inflammation and ill health. Symptoms may include diarrhea, loose stools, abdominal pain, or even constipation.

Overgrowth and excessive colonisation by opportunistic bacteria may occur when the commensal (friendly or beneficial) bacteria are impaired by poor diet, antibiotic use, parasitic infection, or a weakened immune system. When intestinal permeability (or leaky gut) is present, these microbes can cause further damage.


  • Enterococcus faecalis
  • Enterococcus faecium
  • Methanobacteriaceae (family)
  • Morganella morganii
  • Pseudomonas
  • Pseudomonas aeruginosa
  • Staphylococcus
  • Staphylococcus aureus
  • Streptococcus


  • Citrobacter
  • Citrobacter freundii
  • Fusobacterium
  • Klebsiella
  • Klebsiella pneumoniae
  • Mycobacterium avium
  • Prevotella copri
  • Proteus
  • Proteus mirabilis


Fungal organisms are commonly found in the human digestive tract, but fungal overgrowth may only cause symptoms in those who are susceptible or immune-compromised . Fungal growth is localised in the body and can be found the large intestine,  small intestine or elsewhere in the body including, mouth, vagina, nails etc. Stool profiles provide information only about the presence of fungi in the large intestine, and additional tests may be necessary to understand the complete picture of fungal overgrowth. Organic acid profiles (add link) can also provide useful information about the presence of yeast in the body.

  • Candida albicans
  • Candida
  • Geotricum
  • Microsporidia
  • Rhodoturula



  • CMV- Cytomegalovirus
  • EBV- Epstein Bar Virus


A parasite is an organism that lives and feeds on a host organism at the expense of the host. The GI-MAP tests for pathogenic parasites and protozoa most commonly occurring in the GI tract. Sources of exposure should be identified and eliminated to prevent reinfection.


  • Blastocystis hominis
  • Chilomastix mesnelli
  • Cyclospora cayetanenensis
  • Dientamoeba fragilis
  • Endolimax nana
  • Entamoeba coli
  • Pentatrichomonas hominis


  • Ancyclostroma duodenale
  • Ascaris lumbricoides
  • Necator americanis
  • Trichuris trichiura
  • Taenia solium/saginada



This part of the test gives information about how well you are digesting and absorbing your food. Ultimately indicating how well your GI tract is performing its basic digestive functions.

It includes the following markers.

Pancreatic Elastase-1

A check to see how well the pancreas is playing its part in the digestion of protein fat and carbohydrate. Pancreatic elastase is secreted exclusively by the pancreas and provides insight into the production of the digestive enzymes amylase, lipase and trypsin.


Fecal fats are normally broken down by bile salts and absorbed in the small intestines. High levels of fat in the stool may be an indication of maldigestion, malabsorption of dietary fats.



One of the ways that toxins are removed from the body is via the stool – the toxins  are bound to a molecule that allows them to be removed. Beta-glucuronidase can uncouple these toxins resulting in them being recirculated. Beta-glucoronidase can also break down carbohydrates and help the absorption of some plant polyphenols and nutrients.

Occult Blood

The term ‘occult blood’ simply means blood that is not evident to the naked eye and present in microscopic quantities only. Normally, stools should be entirely free of blood. A positive occult blood indicates the presence of free haemoglobin found in the stool, which is released when red blood cells are broken down. Follow-up testing is recommended.


Secretory IgA

SIgA is secreted by the mucosal tissue of the gastrointestinal tract. Mucosal tissue is strategically located in areas where external pathogens enter the body and it helps to form the protective lining or barrier of the digestive tract to protect us against pathogens and bad bugs and toxins.

Anti-gliadin IgA                             

Gliadin is a component of gluten, the protein found in wheat and other field grass grains such as barley, malt, and rye. The presence of fecal anti- gliadin antibodies can indicate an immune response (in the gut) to gluten in the diet. Fecal anti-gliadin antibodies do not necessarily correlate with blood levels.                     



Calprotectin is a simple measure that checks for inflammation in the gut. Calprotectin can be useful for distinguishing between Irritable Bowel Syndrome (IBS) and Inflammatory Bowel Disease (IBD).  Levels can vary with age and children under 10 have higher levels.


Universal Microbiota Antibiotic Resistance Genes.

The GI-Map test checks for antibiotic resistance genes in the microbiome. If an antibiotic resistance gene is present, then that class of antibiotics is designated POSITIVE for antibiotic resistance. A positive result for the presence of resistance genes for a given antibiotic indicates that the antibiotic is not an ideal choice for an antibiotic protocol. Antibiotic resistance genes apply to all of the microorganisms found in the fecal sample. Since microbes can rapidly share DNA under stress, the presence of antibiotic resistance in any organism is reason enough to avoid that drug class.



Zonulin has been identified as a protein that regulates the tight junctions between the epithelial cells lining the digestive tract  – it acts somewhat like a shoelace to pull the cells together. When zonulin is elevated it has been found to be associated with other markers that all together can indicate the presence of intestinal permeability or ‘leaky gut’.

1 single stool sample is required for this profile


You will need to send your sample back to the lab via a next day postal service – If you are in the UK, Royal mail offer a suitable next day service. If you are outside of the UK then please check with your postal service for options. The cost of the test does not cover the return postage.

Please note that samples should only be posted on Monday – Thursday so that they do not arrive over the weekend when the lab is closed.

A courier returns option is offered by the lab and details will be included in with your test kit. This is an optional service and the cost is not included in with the test fee. Details about payment, should you wish to take up this offer, are included with the courier details.

Customers in Germany  – Due to Brexit we have had some issues with postage however the GI MAP is still available and postage is working well as they are sent form a country in the EU.



Adults and children 2 years and above. The child needs to be potty trained and out of nappies. The sample must not be contaminated with urine or fibres from nappies. Please note the reference ranges for digestive and inflammatory markers are for adults.



Refrain from taking digestive enzymes, antacids, and aspirin for two days prior to specimen collection, unless otherwise instructed by your healthcare provider

If taking antibiotics, antiparasitics, antifungals, probiotic supplements (acidophilus, etc.), or consuming food products containing beneficial flora (e.g. Activia®), it is recommended that you wait a minimum of 14 days after your last dose before beginning the test; 28 days may be preferred after antibiotics have been utilized (unless instructed otherwise by your physician). There may be times when your healthcare provider prefers that you stay on one of these agents (e.g. acidophilus) during testing in order to evaluate its effectiveness. Follow your healthcare provider’s recommendation.

Lactoferrin supplements. Whilst lactoferrin supplements will not have a direct impact on the test results they can have an indirect influence owing to the support it provides to the gut wall. Lactoferrin is good for permeability and the overall health of the gut wall. You may like to consider waiting for 72 hours after taking lactoferrin supplements before completing your test samples.

Never discontinue prescription medications without consulting your healthcare provider first.

The test kit will come with full instructions.

How long does it take to get my results?

21 days from samples being received