Gut Microbiome Analysis: Stool Test

Content
1. What is the gut microbiome?
2. Examination of the gut microbiome
2.1 Performing a stool test
2.2 Analysis of a stool test
2.3 When does a stool analysis make sense?
3. Summary

1. What is the gut microbiome?

The gut microbiome is a complex, individual ecosystem of bacteria, archaea, and fungi that plays a crucial role in human health (1, 2). It helps defend against pathogens, produces essential vitamins, hormones, and short-chain fatty acids, and supports the development of the immune system (3-8). The composition of the microbiome varies from person to person and is influenced by factors such as diet, probiotics (live microorganisms in foods), prebiotics (fiber-rich foods), as well as the use of antibiotics and medications (9, 10). A conscious choice of foods can help stabilize the balance in the large intestine and promote a diverse, healthy microbiome.

2. Examination of the gut microbiome

The gut microbiome can be examined using a stool sample, taking advantage of the fact that about one-third of stool mass consists of shed gut bacteria (11). Therefore, analyzing a stool sample is an important method to assess the microbiome and evaluate its condition and composition.

2.1 Performing a stool test

Collecting a stool sample is simple and usually done comfortably at home. The patient receives a special sampling kit that contains everything needed for the safe and hygienic collection of the stool. Following the included instructions, a small amount of stool is placed into the provided tube and securely sealed. The tube can then be sent directly to the laboratory. There, a detailed analysis is performed using modern laboratory methods to precisely identify the bacteria and other important parameters.

2.2 Analysis of a stool test

In the past, cultivating bacteria on agar plates was the only method to determine the composition of the microbiome. However, this approach had limitations because not all bacteria grow under the same conditions: some grow only under anaerobic (oxygen-free) conditions, while others require aerobic (oxygen-rich) environments. Modern techniques like 16S rRNA gene sequencing now provide a more precise and comprehensive analysis. The 16S rRNA gene acts like a “genetic fingerprint” for bacteria. Each bacterial strain carries this specific gene in its DNA, but the sequence varies slightly between species, allowing them to be distinguished from one another. When a stool sample is analyzed in the lab, advanced instruments read the 16S rRNA gene sequence and compare it to known patterns in databases. This enables exact identification of the bacteria present in the gut, even those that are difficult to culture in the lab. Thus, this technique allows for an accurate and thorough analysis of the gut microbiome.
A stool analysis can also measure the pH level of the gut, bacterial diversity, and the distribution of the most common bacterial strains. It provides insight into bacterial metabolic activity, digestive residues (which may indicate potential enzyme deficiencies), signs of inflammation (e.g., through the marker calprotectin), indicators of a “leaky gut” (e.g., through zonulin), as well as the possible presence of parasites. This way, it delivers valuable information about the state of the gut microbiome and overall digestive health.

2.3 When does a stool analysis make sense?

A stool test is useful when there is a suspicion that the gut microbiome is out of balance, for example, in cases of persistent digestive issues such as diarrhea, constipation, bloating, abdominal pain, or food intolerances. The test can help identify potential causes early on, such as an imbalanced gut flora, inflammation of the intestinal lining, a leaky gut, or parasite infestation. It can also provide important clues in cases of recurrent infections, unexplained fatigue, skin problems, or when an enzyme deficiency is suspected. Additionally, the stool test enables the development of a more targeted treatment plan.

3. Summary

A stool test is a valuable diagnostic tool that provides a comprehensive insight into the state of the gut microbiome. It reveals which bacteria are present in the gut, their composition, and how they influence metabolism and digestion. Modern analytical techniques like 16S rRNA sequencing also detect hard-to-culture microorganisms, while important parameters such as pH value, inflammation markers, and potential parasites are measured. This makes the stool test especially useful for digestive issues, food intolerances, recurrent infections, or other health problems. The results help guide targeted measures to support the gut flora, creating an important foundation for sustainable health.

References

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