The Shannon index is a standardised measure used by members of the scientific community to quantify species diversity in an environment (such as an individual’s gut microbiome). Comparing Shannon index values over time can identify changes in diversity.

Polymerase chain reaction (PCR) testing methods extract the DNA from the faecal sample and probe it to identify the tag of a specific bacteria or pathogen. This probing is only carried out for specific microorganisms within the sample and as such cannot provide a complete compositional analysis. Therefore, the spectrum of organisms that can be detected via this method is limited to only a small number of species. However, the method provides high detection sensitivity of specific organisms and if quantitative PCR is used, can also provide a measure of the abundance of detected organisms.

16S rRNA – 16s ribosomal ribonucleic acid (rRNA) sequences a small portion of a single gene found on bacteria. This acts as a fingerprint to identify known bacterial groups but is very similar amongst species, so can only identify down to the genus level. Considering there may be 100 species within any genera, there is no way to determine the health impact of that genus nor its functional metabolites. Likewise, as the method is screening for identified tags of known bacteria, it is unable to detect unclassified bacteria, or other organisms that can be present in the microbiome such as fungi, protists and viruses. It is also important to consider that different labs will use different regions of the gene portion and as such the method is not reproducible across labs.

The MetaBiome™ test uses the latest technology available (shotgun metagenomics) and provides the broadest and most detailed picture of all microorganisms within the microbiome. From a faecal sample, metagenomic sequencing takes in all the genetic material of the gut microbiome. It accurately identifies microorganisms down to the species level; rather than the genus level as many tests currently do, and it looks promising to facilitate strain level detection within the next year. This screening technology is not just limited to detecting known bacteria, but is able to sequence undefined bacteria that will provide valuable insights as more is learnt about them. Likewise, it can accurately sequence genes for all microorganisms and detect levels of viruses, ungi, archaea, protists and parasites, which are just as influential as their bacterial counterparts. This methodology extends beyond compositional analysis to also include functional capacity of the microorganisms present and records their produced metabolites. This provides an understanding of the functional health of the microbiome and its potential to influence the patient’s physiology. As such, metagenomic sequencing is the most reproducible, accurate and comprehensive DNA sequencing method of the microbiome that not only provides an assessment of ‘who is there, but also what they are doing’.

The MetaBiome™ test detects protists and parasites for which there is genomic information available on the Genome Taxonomy Database. For example, Blastocystis can be detected, while Dientamoeba cannot, as there is currently no available genomic information on this parasite. For species where genomic information is available, the test can detect them in abundance over 0.05%.

It is also important to note that parasites are not evenly distributed throughout the stool. As the MetaBiome™ test only uses a tiny amount of faecal material, a parasite will not be detected if it is not present in the stool sample, even if it is present in the individual’s gut. Additionally, the report is not medically diagnostic and is intended for informational purposes only. If a parasitic infection is suspected, consult with a medical practitioner and select a test that collects the whole stool for analysis (e.g. PCR).

There is no need to stop taking probiotics or other supplements before the test, as these are part of the patient’s regular habits and will reflect their “normal” microbiome. In general, maintaining the patient’s regular supplements for two weeks prior to sampling is recommended. Additionally, it is advised to collect a sample from a bowel movement that is typical for that patient in order to capture a “normal” microbiome sample.

Antibiotic use however, is one exception to the rule, as it does affect the microbiome. It is advised that testing should be conducted at least 2 weeks after antibiotic use, once any acute symptoms have resolved.

The score is an indication of the patient’s overall microbiome health, based on the eleven categories listed in the MetaBiome™ report. The contribution of each category to the MetaBiome™ score is weighted according to the level of influence it has on a patient’s health. The current healthy comparison range for the MetaBiome™ score is 98% to 100%.

The score is a specific reflection of microbiome health, and is not indicative of overall gut function. It therefore does not reflect other causes of digestive complaints, such as alterations in motility, absorption of nutrients, and elimination of waste. If the patient has a high MetaBiome™ score but presents with chronic digestive symptoms, this is an indication of a functional cause, rather than an imbalanced microbiome.

Currently the laboratory does not have any information available about these species. This is either because they are new species that are yet to be classified by scientists, or they are uncommon species of the human gut, whose exact function is unknown. The MetaBiome™ report will continue to evolve as new information about these species is discovered.

A high amount (greater than 4%) of human DNA on the MetaBiome™ report suggests increased epithelial cell turnover, indicative of gut inflammation at the time of sampling. However, having low human DNA does not completely exclude leaky gut, as intestinal hyperpermeability can still be present due to reduced tight junction integrity, without overt inflammation.

LPS is an important protective component of the cell wall of many gram-negative bacteria. However, when these bacteria die, their cell walls break down, releasing LPS into the gut where it can have a pro-inflammatory effect.1 Diets high in fat, especially saturated fat, allow LPS to cross the intestinal barrier and enter the bloodstream. This is because lipophilic LPS can incorporate itself into the chylomicrons (small fat globule) that transport dietary fat into the bloodstream.2

LPS comes in two forms – hexa and non-hexa LPS, classified according to molecular weight. Hexa LPS contains six acetyl chains or more (higher molecular weight), while non-hexa LPS contains less than six (lower molecular weight). Hexa LPS is pro-inflammatory and has been associated with diets high in fat, particularly saturated fat.3 It has also been observed in individuals with cardiometabolic conditions, such as heart disease, type 2 diabetes, non-alcoholic fatty liver disease, and obesity.4 Non- hexa LPS has not been associated with any negative health outcomes and may actually exert beneficial effect through immune modulation.

While SCFA production is generally a positive factor, high amounts can indicate an increased abundance of microbial species that are associated with negative health outcomes. For example, Bacteroides fragilis primarily produces succinate and the SCFA, acetate. Although the non-toxic strains of B. fragilis may have beneficial effects, the toxic strains have been correlated with diarrhoeal disease, inflammatory bowel disease flare-ups, and colon disease.6 Thus, increased production of SCFAs may indicate the presence of dysbiotic organisms. Levels of SCFA are therefore optimal when they fall within the appropriate reference range.

This indicates that the patient has microbial species with the capacity to use both fibre and protein as fuel sources. Levels are mostly dependent on the patient’s diet.

BCAAs are building blocks for muscles, and are involved in the regulation of glucose and fat metabolism, as well as the immune system. Despite their health benefits, high blood levels of BCAAs have been associated with obesity, insulin resistance and other metabolic diseases.7 In addition to dietary sources, BCAAs can also be derived from the gut microbiome. Research indicates that an increased microbial gene abundance for BCAA production, is correlated with increased blood levels and may be associated with the aforementioned conditions.

GABA is an important signaling molecule for the brain, with low levels associated with anxiety and depression.9 It is primarily produced by the body, however some bacterial species can also produce (and consume) GABA. Excess GABA may be transmitted from the gut to the brain via the vagus nerve, however the role of bacterially produced GABA is still unknown, and its effects on anxiety and depression is an active area of research.

Trimethylamine is a compound produced by some gut microbes that is converted to trimethylamine-n-oxide (TMAO) in the liver. Increased TMAO levels have been observed in individuals with heart disease, type 2 diabetes, cancer and vascular dementia.10 However, the role of TMAO in these diseases is still unclear, and it is unknown if TMAO is a cause or a marker of these diseases, or if it plays a protective role in repairing damage caused by these diseases.

TMAO levels are influenced by many factors, including the gut microbiome, diet, the integrity of the gut barrier, liver function and kidney function.11 Although diet may play only a small role, diets high in red meat, eggs and salt, have been associated with increased TMAO levels, while diets high in soluble fibre have been shown to reduce trimethylamine and TMAO levels. If your patient’s potential to produce trimethylamine is high, increased consumption of fibre and avoidance of excessive amounts of red meat, eggs and salt is recommended. Additionally, although several gut microbes can produce trimethylamine, some can also use it for energy, thus reducing its levels. Therefore, it is considered beneficial if a patient’s gut microbiome has the potential to consume trimethylamine.

IPA is a potent antioxidant produced by some gut bacteria from the breakdown of the amino acid, tryptophan. Research suggests that IPA is a scavenger of hydroxyl radicals and protects against oxidative damage in different tissues, including the nervous system.12 Animal models also suggest that IPA may play a role in maintaining gut barrier integrity by acting as a ligand for the xenobiotic sensor, pregnane X receptor (PXR).13 Further, low levels of IPA may play a role in the development of type 2 diabetes14 and plasma levels of IPA have also been found to be significantly lower in subjects with Huntington’s disease compared to healthy controls.15 Studies indicate that consuming foods high in dietary fibre (rye-containing foods in particular), can increase IPA production.

Antimicrobial treatment may be considered if the MetaBiome™ report indicates a significant abundance of detrimental species, or if parasitic detection has been reported. In most other cases, optimising the microbiome through the inclusion of pre- and probiotics should be considered the first line treatment.

Hydrogen sulphide gas is a byproduct of the breakdown of sulphur-containing foods, such as eggs, garlic, onion, cabbage, kale or Brussels sprouts, by certain species of the gut microbiome. It can also be produced by bacterial metabolism of bile acids.1 Hydrogen sulphide plays an important role in gut health as an energy source for intestinal epithelial cells, with a protective effect on gut barrier function. However, some studies have suggested that high levels of hydrogen sulphide can also disrupt the mucus barrier of the gut and predispose susceptible individuals to certain health conditions such as inflammatory bowel disease.

Retesting can be conducted after three to six months, depending on the individual case. Many individuals will retest on an annual basis to ensure their microbiome composition remains optimal.