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Comprehensive Microbiome Test – GI Effects Microbial Ecology

Comprehensive Microbiome Test – GI Effects Microbial Ecology

About this test

This Great new health test offers the best way for checking levels of bacteria, yeasts and parasites. Not only does it check by culturing bacteria (Growing it in a petri dish) but it also uses a new technology PCR  –  which looks at the DNA of the bacteria in the stool and is fast becoming the world leader in ways to check 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 this 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 and can be found here.

What is being measured?

The GI Effects Microbial Ecology Profile reports on the commensal (friendly and beneficial) bacteria using both DNA PCR technology and culture technology. It also includes Mycology (yeast species). Further, the profile uses PCR to check for the presence of parasites including Blastocystis Hominis. Additional parasite species may be found using microscopy technology. The test reports any imbalances or infections but not inflammation as suggested on the interpretation at a glance on the sample report.

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

Commensal (Normal) Gut Bacteria

The GI Effects Microbial Ecology Profile takes a detailed look at your 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, but also 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. While 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.

Test results also show the groups and how different diet and lifestyle factors can have an impact on their levels.

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. 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.

How does the test check the Microbiome?

The GI Effects Microbial Ecology tests your microbiome – good and bad bacteria, yeasts and parasites  via:

1 PCR Testing

The most up to date way of testing bacteria is to use a process called PCR – it means that the lab is looking at the DNA of bacteria which is more up to date than trying to culture bacteria – grow them in a petri dish. This is especially 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.

2 Culture

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.

3 Microscopy

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

Please see the comparison table here (coming any day now) 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.

ADD on’s

At the check out you will soon be able to add on the following should you wish b ut if you are interetssd in adding these on now please email admin@smartnutrition.co.uk and we wil be happy to help you.

KOH Preparation for Yeast
This microscopic testing method is used alongside culture to check for yeasts. Results are reported as the amount of yeast detected microscopically measured per HPF – High power field.

Zonulin Family Peptide
Research by Fassano concluded that zonulin acted like a shoe lace to pull the cells of the intestines together. If it was found outside of the reference range it was concluded that it was associated with a leaky gut or intestinal permeability. A recent research paper published in Frontiers in Endocrinology suggested that the zonulin kits from Immundiagnostik (IDK) ( who supply All the labs that we know that run zonulin) did not detect zonulin (a precursor of Haptoglobin 2). This issue was further confirmed by the kit manufacturer, Immundiagnostik. Because some researchers are conducting studies and have received data from the current zonulin kits, Genova are still offering zonulin but have renamed it Zonulin family peptide.

The Scheffler paper suggests that the kits may detect properdin, a protein involved in the alternative complement pathway and inflammation. Preliminary study results from an external investigator suggest that properdin may be structurally and functionally similar to zonulin. When analysing data Genova found a high correlation with raised zonulin and other markers associated with gut mucosal health.

Macroscopy for worms
Most nematodes (roundworms), trematodes (flukes), and cestodes (tapeworms) to a lesser degree, 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.

Helicobacter PyloriEIA. Recent studies have shown that up to 45 – 50% of the world’s population may harbor H. pylori. Many carriers are asymptomatic, but H. pylori is known to have a causative role in ulcers, chronic gastritis, and stomach cancer. Direct stool testing of the antigen (HpSA) is highly accurate and is appropriate for diagnosis and follow-up of infection.

Campylobacter spp – EIA. Campylobacter jejuni is the most frequent cause of bacterial-induced diarrhea. While transmission can occur via the fecal-oral route, infection is primarily associated with the ingestion of contaminated and poorly cooked foods of animal origin, notably, red meat and milk. Symptoms range from mild to severe abdominal pain, diarrhea, fever, malaise; lasting several days to several weeks.

Clostridium difficile  EIA. Clostridium  Difficile also known as C.Diff  is an anaerobic, spore-forming gram-positive bacterium. Changes in gut flora, usually caused by antibiotics can lead to colonization with Clostridium difficile. Symptoms include inflammation, abdominal pain, cramping, fever, and diarrhea. Symptoms often present during antibiotic use and often subside once antibiotics are discontinued.

E. coli EIA is a group of bacterial strains that have been identified as worldwide causes of serious human gastrointestinal disease. Enterohemorrhagic E. coli includes over 100 different serotypes; 0157:H7 is the most significant, occurring in over 80% of all cases. Contaminated food continues to be the principal vehicle for transmission; foods associated with outbreaks include alfalfa sprouts, fresh produce, beef, and unpasteurized juices. The symptoms may include severe abdominal cramps and diarrhea and bloody diarrhea.

Fecal Lactoferrin;
In the gastrointestinal tract, lactoferrin serves as a non-specific marker of inflammation

Type of specimen required for the test

1 or 3 day collection with 6 vials or tubes to complete

The lab recommends samples are collected on 3 consecutive days but if this is not possible they should be collected over a week. If this is not possible please do get in touch to discuss this.

Age range this test is suitable for

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.

Before taking this test

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.

Never discontinue prescription medications without consulting your healthcare provider first.

The test kit will come with full instructions.

Returning your sample

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 offers 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 with the test fee. Details about payment, should you wish to take up this offer, are included with the courier details.

How long does it take to get my results?

19 Working days

All sample reports are for representational and educational purposes only. Biomarkers, references ranges, results, and all other data may differ from actual reports. All data included in no way rpresents an actual patient. Any comparisons of results to actual patients, is completely incidental. 

Smart Nutrition GI Effects Microbial Ecology Sample Report – Updated September 2020