How to Read a Gut Microbiome Report

A gut microbiome report can look like a lot at first: bacteria with Latin names, scores, charts and coloured bars. The good news is that most reports are built from a small number of ideas. Once you know what each section is trying to show, the whole thing becomes much easier to read.

This guide uses the layout of our own GI Axis report as the example, but the principles apply to most stool-based microbiome tests.

First, what the test measures

A microbiome test reads the DNA of the microbes in a small stool sample. Our laboratory uses shotgun metagenomics, which sequences the genetic material in the sample and matches it to a reference library. That lets the report name the bacteria it finds and estimate how much of each is present compared with the others.

It is a snapshot. Your microbiome shifts with what you eat, recent illness, antibiotics, travel and stress, so a result describes your gut on the day you took the sample. It is also not a diagnosis. Think of it as information to use with your symptoms and your practitioner.

Diversity: how varied is your gut community?

Diversity is usually the first number in a report. It describes how many different types of bacteria you have and how evenly they are spread. Our report uses the Shannon index, a standard measure borrowed from ecology.

In general, higher diversity is associated in research with a healthier gut, much as a woodland with many species tends to be more resilient than a single-crop field. Low diversity is often seen after antibiotics, in people on very limited diets and in some digestive conditions. There is no single perfect score, though, and a lower reading does not mean something is wrong with you. It is a prompt to look at the other parts of the report, and a number you can compare with a repeat test later.

Key bacteria: who is there?

Next you will see individual bacteria or groups. Our report highlights 17 significant bacteria. Instead of trying to learn each name, read them in terms of what the group does:

• Bacteria that produce short-chain fatty acids, such as butyrate. These help nourish the cells that line the bowel, and low levels are often discussed in relation to gut health.
• Bacteria linked to inflammation, which may be higher in some people with digestive complaints.
• Bacteria that break down particular foods, for example fibre, protein or fat, which tells you something about how your gut handles your diet.
• Hydrogen producers, which are linked to gas and bloating.

Reports normally show each bacterium relative to a reference range. A bar sitting outside the range is something to note, not a reason for alarm.

Markers and indices

Beyond individual species, a report may include summary scores built from several findings. The GI Axis report includes, among others:

• an intestinal permeability index, which estimates how the pattern of bacteria relates to the integrity of the gut barrier
• a calprotectin-linked dysbiosis score, which looks at a bacterial pattern associated with gut inflammation
• an antibiotic degradation marker
• a cardiovascular health marker linked to TMAO, a compound made by gut bacteria from certain nutrients

These are indirect markers based on bacterial patterns, not direct clinical measures. A stool calprotectin test ordered by a doctor, for example, is a different thing from a score estimated from bacterial DNA. If a score concerns you, take it to your GP.

Gut health axes

Some reports group findings into “axes”, which describe how the gut relates to other parts of the body, such as skin, brain, metabolism or the thyroid. The research on these links is growing but varies in strength from one axis to another. Read them as areas where your gut pattern may be worth attention, particularly if you also have symptoms in that area.

Putting it together

A practical way to approach your report:

1. Start with the summary pages and your diversity result.
2. Note the flagged items, meaning those outside the reference range.
3. Match them to your symptoms. A finding that lines up with something you experience is more useful than one that does not.
4. Look at the suggestions for diet and lifestyle and choose one or two to start, instead of changing everything at once.
5. Share it with a practitioner, who can weigh it with your history and any other tests.
6. Retest when it suits you. Many people repeat after a few months of changes to see what has moved.

Common mistakes

Reading too much into a single bacterium is the most common one. Others include comparing your numbers with someone else’s, assuming an out-of-range value must be fixed with a supplement and treating the report as a diagnosis. If you have red-flag symptoms such as blood in your stool, unexplained weight loss or persistent changes in bowel habit, speak to your GP before anything else.

See what a report looks like

Our GI Axis report covers diversity, 17 significant bacteria, core metrics and ten gut health axes. GI Axis Advanced adds the GI Axis Microbial Screen, which looks for 28 additional markers across fungi, parasites, pathogenic bacteria, viruses and archaea. You can browse all of them in the shop.