Digestive Stool Test GI Effects Gut Microbiome

Digestive Stool Test GI Effects Gut Microbiome

This comprehensive microbiome health test offers the best way for checking levels of bacteria, yeasts and parasites. It checks by culturing bacteria (growing it in a petri dish) as well as using PCR technology which looks at the DNA of the bacteria in the stool, and is fast becoming the world leader in methods for checking for bacteria and parasites.

The GI Effects Microbial Ecology Profile offers a comprehensive look at the gut microbiome.

It provides insight into gastrointestinal microbial abundance and balance, including good and potentially bad or harmful bacteria as well as looking for the presence of yeasts including candida, parasites and worms.

This smaller profile is part of the larger GI Effects Comprehensive Profile which you can find here. This other test also provides information about digestion, inflammation and bacterial metabolism markers.

Markers of inflammation are not covered in the GI Effects Microbial Ecology Profile despite it showing on the test result. Absence of reported markers doesn’t exclude inflammation. If you suspect current inflammation, please consider the GI Effects Comprehensive Profile here, which does report on gut inflammation. The Genova Diagnostics Calprotectin Profile is another, smaller option, which simply reports on inflammation. It can be found here.




The GI Effects Microbial Ecology Profile reports on the commensal (friendly and beneficial) bacteria using DNA, PCR technology and culture technology. It also includes mycology (yeast species). The profile uses PCR to check for the presence of parasites including Blastocystis hominis. Additional parasite species may be found using microscopy technology.

PCR testing:

The most up to date way of testing bacteria is to use a process called PCR, which means that the lab is looking at the DNA of bacteria. It is more sophisticated than trying to culture bacteria (grow them in a petri dish), which is important as many bacteria are anaerobic, meaning they do not live in oxygen and therefore die soon after they have left the body. This makes culturing many bacteria impossible.


The process of culturing means that the lab checks for the presence of good, bad and imbalanced bacteria and yeasts by trying to grow them in a petri dish. If they manage to grow any bacteria or yeasts such as candida, they then treat them with pharmaceutical and natural antimicrobial agents to see which are sensitive, meaning which are reduced or killed off by the agent.


Highly skilled lab technicians check for eggs and parasites and yeast with a microscope.

Please see the comparison table to see exactly which good and bad bacteria, yeasts and parasites are checked for on the GI Effects, or check out the sample report at the bottom of the page.

The test reports any imbalances or infections but not inflammation as suggested on the interpretation at a glance on the sample report. Please see the link in the introduction for links to tests which do test for inflammation.

As well as checking for imbalances and infection the test also checks for;

Commensal (normal) gut bacteria

It checks for 7 Phyhla – groups of bacteria and 24 main species.

Commensal bacteria form a part of what makes up your microbiome. It is made up of trillions of microorganisms along with commensals, and including good, bad and imbalanced bacteria, yeasts and, for some, also parasites. Your microbiome 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. When in balance, commensal bacteria all live happily together and play important roles in health and or digestion. Research has demonstrated the bacteria in the gut interact with the immune system and play an important part in immunity.

The test uses algorithms and data collected over the past years, meaning the lab is able to report on various observations about your commensal bacteria such as abundance, immune versus inflammatory susceptibility, diversity and balance.

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 (associated with leaky gut)
  • Modulating oxidative responses
  • Producing vitamins (e.g. biotin, vitamin K)
  • Metabolising xenobiotics and phytochemicals (removing toxins)
  • Preventing colonisation by potential pathogens

Commensal balance score

Low levels are often seen after antimicrobials or antibiotics or in diets lacking in fibre. Higher levels may indicate an overgrowth of beneficial bacteria or the effects of probiotic supplementation.  If probiotics are not stopped before testing, as instructed, levels may be very high.

Relative abundance – phyla

Bacteria are grouped into families called phyla and your results will cover the seven major phyla and are compared to a healthy cohort/ group.


Bacteria and mycology (yeast) sensitivity

In the ever-expanding world of microbial resistance, the sensitivity panel is a valuable tool to help inform which antimicrobial drugs or plant based antimicrobials may be most effective in addressing any imbalances and /or pathogens.

Clostridium difficile (not available for patients <2 years old)
Escherichia coli
Helicobacter pylori
Feacal lactoferrin
Macroscopic Exam for Worms
Zonulin Family Peptide
KOH Preparation for Yeast

Zonulin Family Peptide
Zonulin has been identified as a protein that regulates the tight junctions between the epithelial cells lining the digestive tract, acting 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”.

Macroscopy for worms – See Worms – Macroscopic test details . This test needs to be ordered separately.
Most nematodes (roundworms), trematodes (flukes), and, to a lesser degree, cestodes (tapeworms), are primarily diagnosed by ova in the stool during the microscopic O&P exam which is included as standard on this test. The macroscopy for worms add on is an examination of the entire specimen to look for macroscopic evidence of proglottids (tapeworm segments) or whole worms prior to doing the microscopic examination.

If a patient sees worms in the stool, they should remove the worm from the stool and place it in the vial clean of any stool, or in a separate container for transport to the lab.


Stool samples collected over 3 days.

If a patient sees worms in the stool, they should remove the worm from the stool and place it in the vial clean of any stool, or in a separate container for transport to the lab.

Women should not collect samples while menstruating.

Do not collect if you have bleeding from haemorrhoids.

4 weeks before your test:

Wait 4 weeks from having a colonoscopy or barium enema before starting the test.

2 weeks before your test:

Wait until you have finished any course of antibiotics, antiparasitics, antifungals, probiotic supplements (acidophilus, etc.) or consuming food products containing beneficial flora (e.g. Activia®).

2 days before your test:

Refrain from taking digestive enzymes, antacids, and aspirin for two days prior to specimen collection, unless otherwise instructed by your GP or practitioner.

Lactoferrin supplements will not have a direct impact on the test results, but can have an indirect influence owing to the support they 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 GP or practitioner provider first.


Please return via a next day service Monday – Thursday only. The samples must be stored in the fridge prior to returning.

A courier option is sent with your test kit. You pay the laboratory directly for this test and also the return courier if you use the service. You can also make your own arrangements for returning your samples via a next day service.

17 – 19 working days.

Your test results will be emailed to you.

Digestive Stool Test GI Effects Gut Microbiome