Basic gut profile – stool test for microbiome, leaky gut & histamine

Calprotectin is a protein from white blood cells (neutrophils). When many of them enter the intestinal lining, calprotectin in stool rises. The value is therefore used as a marker of inflammation in the gut, for example to distinguish chronic inflammatory bowel diseases from irritable bowel syndrome (PubMed 31088326). In a meta-analysis of 17 studies, calprotectin distinguished these two groups well; an elevated value alone, however, is not proof of an inflammatory disease (PubMed 37823411).

Alpha-1 antitrypsin is a blood protein. If more of it is found in stool, this can indicate protein loss via the gut, as occurs with inflamed or altered mucosa (PubMed 20571826). Elevated values of either marker should be checked by a doctor.

Zonulin is a protein that can loosen the connections between the cells of the intestinal lining (tight junctions). When more zonulin is present, the gut wall can become more permeable (PubMed 21248165). That is why zonulin in stool is measured as a marker of the gut barrier and of "leaky gut".

Important for interpretation: a 2018 study showed that a widely used commercial zonulin assay does not detect zonulin itself but related proteins such as properdin (PubMed 29459849). The value is therefore an indication, not proof of a permeable gut wall. Secretory IgA (sIgA) is the most important antibody of the mucous membranes and binds pathogens before they reach the lining (PubMed 21975936); a high value can indicate an activated mucosal defence, a low value a weaker one.

Histamine is formed in the gut, among other things, when bacteria convert the amino acid histidine, and it occurs in foods such as aged cheese, wine or sauerkraut. It is broken down mainly by the enzyme diamine oxidase (DAO) in the intestinal lining (PubMed 33921522).

An elevated value in stool shows that there is a lot of histamine in the gut. In one study, the gut flora of some people with irritable bowel syndrome produced particularly large amounts of histamine; in mice colonised with this flora, the pain sensitivity of the gut increased (PubMed 35895832). For the question of histamine intolerance there is the histamine and DAO analysis.

Yeasts such as Candida albicans are part of the normal gut flora in small amounts in many healthy people (PubMed 36135388). The report shows whether Candida species, Geotrichum candidum and moulds are detectable and in what amount.

Larger amounts can occur, for example, after antibiotics or with weakened immunity. Research is investigating the role of Candida in chronic inflammatory bowel diseases (PubMed 39735273). A distinct "Candida syndrome" with general complaints is not scientifically established.

The basic profile determines the gut flora by culture, i.e. by growing it in the laboratory, and states the bacterial count per gram of stool. The aerobic bacteria are E. coli, enterococci and bacteria such as Klebsiella, Proteus, Pseudomonas, Enterobacter, Serratia and Hafnia, which normally occur only in small amounts. The anaerobic bacteria are Bifidobacterium, Bacteroides, Lactobacillus and clostridia. In studies of irritable bowel syndrome, Bifidobacterium and Faecalibacterium were reduced and Enterobacteriaceae increased (PubMed 30940523).

In addition, two bacteria are measured by molecular methods (PCR): Faecalibacterium prausnitzii, an important producer of butyrate that was found in lower amounts in Crohn's disease (PubMed 18936492), and Akkermansia muciniphila, which lives in the mucus layer and was more often found in lower amounts in overweight and metabolic disorders (PubMed 39940420).

The digestive residues show how much fat, nitrogen (from protein), sugar and water remain in the stool. If a lot of fat remains, this is called fat malabsorption; it can be due to problems with the pancreas, bile acid metabolism or the intestinal lining (PubMed 38429963).

Pancreatic elastase is an enzyme of the pancreas. A low value can indicate reduced enzyme production (exocrine pancreatic insufficiency), which can show up as fatty stools, bloating, abdominal pain, diarrhoea and unintended weight loss (PubMed 37737818). Bile acids in stool are studied in connection with chronic diarrhoea; bile acid loss was found in up to 40% of people with diarrhoea-predominant irritable bowel syndrome (PubMed 26913381). Such values should be interpreted by a doctor.

Stool pH reflects the environment in the large intestine. When gut bacteria ferment dietary fibre, short-chain fatty acids such as butyrate are produced and the pH falls (PubMed 11427691). The report also describes the colour and consistency of the stool.

A rather high (alkaline) value can indicate that little fermentation is taking place, for example with a low-fibre diet; a very low (acidic) value can indicate strong fermentation, for example when carbohydrates such as lactose are not fully absorbed in the small intestine. pH alone does not allow a diagnosis.

The intestinal lining is a barrier: it lets nutrients through and holds back bacteria, toxins and undigested food components. "Leaky gut" describes a gut wall that is more permeable than usual (PubMed 31076401).

A review lists documented influences including endurance exercise, painkillers from the NSAID group, certain food additives and inflammatory bowel diseases (PubMed 31076401). The term is colloquial; a distinct "leaky gut syndrome" as a diagnosis is not established.

The basic profile determines most bacteria by growing them in the laboratory (culture) and counts selected key bacteria. A molecular-genetic microbiome analysis, in contrast, reads the genetic material of the bacteria directly from the sample and captures many more species, including those that cannot be cultured. This depth is offered by Microbiome Maxi Plus, for example.

Both methods provide a snapshot: the gut flora fluctuates from day to day and differs in every person (PubMed 40276224). The report therefore always states the laboratory's method and reference range.

Some values of the basic profile are well established in medicine, such as calprotectin for inflammation (PubMed 31088326) and pancreatic elastase for pancreatic function (PubMed 37737818). Others, such as zonulin, are disputed as a measure (PubMed 29459849), and there are no generally valid "healthy" values for the gut flora.

The test therefore provides indications that need to be interpreted in the context of complaints and previous findings. It does not provide a diagnosis and does not replace a colonoscopy or bowel cancer screening.

Research associates the markers of the basic profile with the following complaints and conditions, with varying strength of evidence:

• Irritable bowel syndrome with abdominal pain, bloating, distension, diarrhoea or constipation: altered gut flora and, in some patients, a more permeable gut wall, observed in studies (PubMed 30940523, PubMed 28404070).
• Chronic inflammatory bowel diseases such as Crohn's disease and ulcerative colitis: elevated calprotectin in stool, well documented (PubMed 31088326).
• Fatty stools, diarrhoea and weight loss with reduced pancreatic function: well documented (PubMed 37737818).
• Chronic diarrhoea due to bile acid loss: described in reviews (PubMed 26913381).
• Histamine intolerance with bloating, headache, flushing or itching after histamine-rich meals: described, the diagnosis is difficult (PubMed 17490952).
• Skin problems such as acne or atopic dermatitis: discussed via the "gut-skin axis", so far mainly in reviews (PubMed 40050613).
• Stress and exhaustion: links between stress and the gut barrier are being studied (PubMed 36806451).

These are associations from studies, not causes in an individual. A stool test cannot explain complaints and does not provide a diagnosis. Persistent complaints should first be checked by a doctor.

With blood in the stool or black stool, unintended weight loss, fever, diarrhoea at night, severe or new abdominal pain, persistent vomiting or difficulty swallowing, the first step is a doctor's practice, not a self-test. The same applies if your bowel habits change for the first time from around age 50 or if bowel cancer, coeliac disease or chronic inflammatory bowel disease runs in the family.

If you suspect coeliac disease, do not stop eating gluten before the medical work-up, because the tests may otherwise come back falsely normal. A stool test does not replace bowel cancer screening.

This page does not give treatment recommendations. Whether a result means anything at all and which steps make sense depends on your overall situation: complaints, previous findings, medication and diet. That complaints improve by restoring the gut barrier has not yet been shown (PubMed 31076401).

What makes sense for you belongs in a conversation with the ORY expert team or with your doctor or naturopath, for example from the ORY expert network. The results consultation is included in the price.

No antibiotics for 4 weeks beforehand, no laxatives, colon cleansing or colonoscopy for 2 weeks beforehand, no probiotic supplements for 1 week beforehand (yoghurt and kefir are allowed) and no major change in diet such as fasting for 3 days beforehand. Only pause prescribed medication after talking to your doctor.

Do not collect the sample during menstruation; ideally collect it in the morning. It must not come into contact with urine or toilet water. Store it in the fridge until shipping (do not freeze) and send it from Monday to Thursday.

Analysis usually takes 7–21 days from the arrival of the sample at the laboratory. Afterwards we offer you a free 10-minute discussion of the results. As soon as your report is ready, we let you know. A results consultation with the ORY expert team is included in the price.

The basic gut profile costs €285 including VAT, shipping, return postage and results consultation.

Statutory health insurance in Germany generally does not cover stool analyses you order yourself. With private insurance, reimbursement may be possible; how it works is described under "Reimbursement by private insurance".

The basic gut profile (€285) combines gut flora, Candida, pH, leaky gut and inflammation markers, histamine and digestion. The gut profile microbiome & gut barrier (€315) sets different priorities among the key bacteria. Gut barrier & absorption (€179.90) measures only gut barrier, inflammation and digestion, without the gut flora. Microbiome Maxi Plus (€285) analyses the gut flora by molecular genetics; Microbiome Maxi Plus + gut barrier + absorption (€465) combines both. For children there is the gut check-up for children (€315), for histamine alone the histamine and DAO analysis (€93).

Which scope makes sense for you can be clarified in the free initial consultation.