4 / Gut Tests: What Is Actually Worth Checking?

You have worked on the foundations. You have looked at fibre, food diversity, bowel habits, meal patterns, movement, stress and the supplements you may or may not need. But perhaps you are still persistently bloated, your bowel habits remain unpredictable, certain foods continue to cause problems or something simply doesn't feel right.

This is where testing can become useful. But as with every other area we have covered, I don't believe in testing simply because a test exists. Gut testing should answer a specific question: Are we looking for inflammation, infection, malabsorption, coeliac disease, pancreatic dysfunction, SIBO or another condition that would actually change what we do next?

And sometimes the most useful investigation isn't a stool test at all.

Start with the symptoms, not the laboratory

Before ordering anything, the pattern of your symptoms matters enormously. Persistent diarrhoea requires a different investigation from chronic constipation. Reflux needs a different approach from unexplained weight loss. Bloating after certain carbohydrates raises different questions from greasy, difficult-to-flush stools accompanied by weight loss.

Age, family history, medications, previous gastrointestinal disease, travel, surgery and how long the symptoms have been present all help determine what should be investigated.

This is why a huge "comprehensive gut panel" isn't necessarily comprehensive in any clinically useful sense. It may measure an impressive number of things while completely missing the question your symptoms are actually asking.

Basic blood tests can tell us a surprising amount

Before analysing hundreds of organisms in your stool, some fairly ordinary blood tests can provide useful clues.

A full blood count can identify anaemia and may reveal other abnormalities that warrant investigation. Ferritin and iron studies become particularly important when iron deficiency is suspected. Iron deficiency may result from heavy menstrual bleeding in perimenopause, but gastrointestinal blood loss or impaired absorption also needs consideration, particularly when the cause isn't obvious.

Depending on symptoms, vitamin B12 and folate can help assess possible nutritional deficiency or malabsorption. Liver markers can provide clues when symptoms suggest liver or biliary disease, while renal function and electrolytes may be relevant with persistent diarrhoea or other systemic symptoms.

CRP, an inflammatory marker, can sometimes help identify evidence of systemic inflammation, although an elevated result does not tell us where that inflammation is coming from. It is another clue, not a diagnosis.

And because hypothyroidism can contribute to constipation while hyperthyroidism can cause more frequent bowel movements or diarrhoea, TSH with appropriate additional thyroid testing can sometimes belong in a gastrointestinal investigation too.

The gut does not exist independently from the rest of your physiology.

If coeliac disease is possible, test before removing gluten

This one is important because many people remove gluten as their first response to bloating.

Coeliac disease is an autoimmune disease triggered by gluten in genetically susceptible people. It can cause diarrhoea, bloating and abdominal discomfort, but it can also present with iron-deficiency anaemia, fatigue, osteoporosis, nutrient deficiencies or relatively subtle gastrointestinal symptoms.

Initial investigation commonly includes tissue transglutaminase IgA, or tTG-IgA, together with total IgA. Additional tests may be used depending on the results and individual circumstances.

But there is a catch: you need to be eating gluten for coeliac testing to work properly. If you remove gluten for months before testing, antibody concentrations may fall and the results can become misleading.

So if gluten appears to cause problems and coeliac disease is a possibility, investigate first. Don't make a gluten-free diet the diagnostic test.

Faecal calprotectin can help us distinguish inflammation from IBS

Persistent diarrhoea, abdominal pain and altered bowel habits can occur in both irritable bowel syndrome, IBS, and inflammatory bowel disease, IBD, but these are very different conditions.

IBS is a disorder of gut-brain interaction and does not cause the intestinal inflammation and tissue damage characteristic of Crohn's disease or ulcerative colitis.

This is where faecal calprotectin can be useful. Calprotectin is released predominantly by neutrophils, a type of immune cell, and increased concentrations in stool can indicate intestinal inflammation.

A low result can make active inflammatory bowel disease less likely in the appropriate clinical setting, while a significantly elevated result may indicate that further investigation is needed.

But calprotectin isn't an "IBS test." It can also rise with gastrointestinal infections, some medications and other inflammatory conditions. The result has to be interpreted alongside symptoms and medical history.

Again, the test answers a question. It doesn't diagnose the entire gut.

Stool testing for infection has a specific purpose

If diarrhoea begins suddenly, particularly after travel, contaminated food or water, antibiotic use or exposure to somebody with gastrointestinal infection, stool testing may be appropriate.

Depending on the situation, testing can look for particular bacteria, parasites or bacterial toxins, including Clostridioides difficile when clinically relevant.

This is very different from screening an otherwise well person for dozens of organisms simply to see what appears.

Your intestine normally contains an enormous number of microorganisms. Finding microbial DNA in stool does not automatically mean the organism is causing disease.

The clinical context determines whether a detected microorganism matters.

H. pylori is worth knowing about

Helicobacter pylori, usually shortened to H. pylori, is a bacterium that colonises the stomach. Chronic infection can cause gastritis and peptic ulcers and increases the risk of gastric cancer.

Testing becomes particularly relevant with certain upper gastrointestinal symptoms or a history of peptic ulcer disease, iron deficiency in some circumstances and other recognised clinical indications.

Two useful non-invasive tests are the urea breath test and stool antigen test. Both can detect active infection.

There is an important practical detail: proton pump inhibitors, antibiotics and bismuth-containing medicines can interfere with testing and potentially produce false-negative results. Appropriate timing and preparation therefore matter.

If H. pylori is found, this is not something I would try to "balance" with probiotics or a herbal gut cleanse. It requires appropriate eradication treatment and confirmation that the infection has been successfully cleared.

What about SIBO?

Few digestive diagnoses have become as popular online as small intestinal bacterial overgrowth, or SIBO.

SIBO occurs when excessive numbers or abnormal populations of bacteria are present in the small intestine. Symptoms can include bloating, abdominal discomfort, diarrhoea and sometimes constipation, but these symptoms are extremely nonspecific and overlap considerably with IBS and other gastrointestinal conditions.

Breath testing usually measures hydrogen and methane after consuming a test substrate such as glucose or lactulose. The gases are produced by microorganisms and absorbed into the bloodstream before being exhaled.

Breath tests can be clinically useful in selected situations, but they have important limitations. Preparation, intestinal transit time, the substrate used and interpretation criteria can all influence the result. A positive test therefore needs to make sense in the context of the person's symptoms and risk factors.

I would not test every bloated woman for SIBO.

And I certainly wouldn't repeatedly treat presumed SIBO without asking why it developed or why symptoms keep returning.

Pancreatic elastase answers a very different question

The pancreas produces digestive enzymes needed to break down fats, proteins and carbohydrates. When it fails to produce sufficient digestive enzymes, a condition called exocrine pancreatic insufficiency can develop.

Symptoms may include chronic diarrhoea, greasy or difficult-to-flush stools, weight loss, nutritional deficiencies and difficulty absorbing fat.

Faecal elastase is a stool test that can help assess pancreatic exocrine function. A low result may suggest pancreatic insufficiency and lead to further investigation.

This is a good example of targeted testing. Pancreatic elastase can be extremely useful when the symptoms fit. It is considerably less useful as a routine marker in every person with occasional bloating.

What about testing for lactose intolerance?

If milk repeatedly causes bloating, abdominal discomfort, gas or diarrhoea, lactose malabsorption may be worth considering.

Lactose normally needs to be broken down by the enzyme lactase in the small intestine. When lactase activity is insufficient, lactose reaches the colon where bacteria ferment it, producing gas and drawing water into the bowel.

A hydrogen breath test can help identify lactose malabsorption, although in some situations a carefully structured dietary trial may also provide useful information.

And remember that lactose intolerance does not necessarily mean avoiding all dairy. Many people tolerate lower-lactose foods such as hard cheeses or particular yoghurts perfectly well.

The aim is not to eliminate an entire food group unnecessarily.

Do you really need a microbiome test?

This is where I become much more cautious.

Commercial microbiome tests can identify large numbers of bacteria and other microorganisms in a stool sample. Some then provide diversity scores, ratios, lists of supposedly beneficial and undesirable organisms and personalised food or supplement recommendations.

The technology used to identify microbial DNA is impressive.

Our ability to translate all of that information into reliable individual treatment decisions is much less impressive.

The gut microbiome varies considerably between healthy people. Diet, medication, geography, age and many other factors influence its composition. We also do not currently have universally accepted reference ranges defining the ideal abundance of most microbial species in an individual person.

A result saying you have "low" levels of one bacterium or an unfavourable ratio between two groups does not necessarily mean you have a disease that needs correcting.

This doesn't make microbiome research useless. Far from it. It is one of the most fascinating areas of medicine.

But research capability and clinical usefulness are not the same thing.

If a commercial microbiome test gives you twelve pages of results but we don't know whether changing those numbers improves your health, I question how much actionable information we have actually gained.

And what about comprehensive functional stool panels?

Some functional stool panels combine microbial analysis with markers of inflammation, digestion, immune activity and other measurements.

Parts of these panels may contain genuinely useful information. The problem is when validated clinical markers and much less established markers are presented together as though every result has equal diagnostic significance.

That can lead to a perfectly healthy microbial variation being labelled "dysbiosis," followed by restrictive diets, antimicrobials and long supplement protocols designed to normalise numbers whose clinical significance may be uncertain.

Look widely. Understand systems. Ask why. But also know what a test can and cannot tell you.

When an endoscopy tells us more than another stool test

Sometimes the next investigation needs to actually look at the gastrointestinal tract.

An upper gastrointestinal endoscopy, or gastroscopy, allows a clinician to examine the oesophagus, stomach and first part of the small intestine and obtain biopsies where necessary. It may be indicated with symptoms such as persistent swallowing difficulty, gastrointestinal bleeding, certain persistent upper gastrointestinal symptoms or other concerning findings.

A colonoscopy allows direct examination of the colon and can identify polyps, cancers, inflammatory bowel disease and other abnormalities while also allowing biopsies or removal of polyps.

Whether these investigations are appropriate depends on symptoms, age, screening recommendations, family history and other risk factors.

The important point is that there comes a stage where repeatedly testing blood and stool is less useful than actually looking at the tissue.

Gut tests: know which symptoms require further investigation

Most bloating, constipation and intermittent digestive discomfort will not turn out to represent serious gastrointestinal disease. But certain symptoms change how quickly and how thoroughly we should investigate.

Visible blood in the stool, black stools, unexplained iron-deficiency anaemia, unintended weight loss, persistent vomiting, progressive difficulty swallowing, significant persistent abdominal pain or a new persistent change in bowel habits deserve medical assessment.

Family history matters too, particularly a strong history of colorectal cancer, inflammatory bowel disease or coeliac disease.

And new persistent symptoms should not automatically be dismissed because you happen to be going through menopause. Menopause may influence digestion, but it does not automatically explain a new gastrointestinal problem.

So what would I actually check?

There is no universal "gut panel." I would choose investigations according to the dominant symptoms and the question we are trying to answer.

A starting assessment may include full blood count, ferritin and iron studies, CRP, thyroid function, B12 and folate, liver and renal markers where appropriate. Coeliac serology becomes important when symptoms, iron deficiency or other features raise suspicion of coeliac disease.

For persistent diarrhoea or concern about intestinal inflammation, faecal calprotectin may be useful. Stool testing for infection should be guided by symptoms and exposure. H. pylori testing, breath testing for SIBO or lactose malabsorption, and faecal pancreatic elastase all have potential roles when the clinical picture specifically points in those directions.

And sometimes the appropriate next step is not another laboratory test at all. It is referral for imaging, endoscopy, colonoscopy or specialist assessment.

The principle is simple: don't ask what gut tests are available. Ask what you are trying to find out.

What I want you to take away from this series

Good gut health is not about achieving perfect stools, eliminating every food that ever caused bloating or creating a flawless microbiome report. It starts with understanding how digestion works, identifying your dominant symptoms and supporting the basic physiology with appropriate food, fibre, movement, sleep and dietary diversity.

When symptoms persist, investigate intelligently. Test for a reason, interpret the result in context and treat what you actually find rather than everything that could theoretically be wrong. And if symptoms suggest something more significant, move beyond "gut health" and into proper medical investigation.

You can explore more articles, free and paid resources, my book and programmes in the Gut & Digestion section of Feel Good Menopause.