What is portioned here under a kind of oversized extractor hood and largely behind a glass pane was once breakfast, lunch or dinner. When the stool samples delivered from doctors’ practices and hospitals arrive at the Bioscientia laboratory in Ingelheim around midday, the material is first divided.

One part is used to create cultures for bacteria such as Salmonella and Campylobacter, the other is prepared for so-called PCR tests – test procedures for detecting specific gene sequences – as laboratory doctor Gergely Bodis explains.

What happens then is, so to speak, detective work: Many viruses, bacteria and parasites can cause gastrointestinal problems and diarrheal diseases. One of the most well-known pathogens are noroviruses, of which the Robert Koch Institute (RKI) records tens of thousands of cases in Germany each year. But in the end, according to the RKI, they are only responsible for a maximum of around half of non-bacterial infections of the gastrointestinal tract. It is therefore important to find the actual culprit from a wide range of possibilities.

Various tests

The technology is now so advanced that samples can be examined for a good two dozen common pathogens in one fell swoop using so-called multiplex PCR analyses. A team from the Frankfurt University Hospital compared such analyzes with conventional methods. According to the study published in February, the detection rate was higher and the results were available more quickly. In addition, the broader approach enables chance hits – i.e. detects pathogens that the doctor may not have even suspected.

PCR tests cannot provide any information as to whether pathogens are resistant to antibiotics. “Therefore, if necessary for targeted therapy or for outbreak surveillance and control, samples must continue to be cultured,” the study said.

In the Bioscientia laboratory, the classic Petri dishes with mostly colorful culture media are also stacked on the tables. This checks whether there are viable bacteria in a stool sample, as doctor Bodis explains. There are now more and more people who, out of interest in their bodies, are looking into the microbiome of their intestines – i.e. the composition of the microorganisms there.

Problem: There is no standard

Some people use test kits in the hope that the results will help them identify problems or make targeted adjustments to their own diet. However, the German Society for Gastroenterology, Digestive and Metabolic Diseases advises against such self-tests. Among other things, because they are not standardized and difficult for users to interpret.

It makes a big difference where in the intestine the stool comes from, explains Bonn specialist Birgit Terjung. To date, there is no established standard as to what constitutes a healthy intestinal microbiome. The microbiome also varies comparable to a fingerprint. It is therefore problematic to derive further recommendations from the results of such test kits, such as changing your diet or taking nutritional supplements.

For a conventional analysis, a small amount of feces is sufficient, says Bodis: the size of a hazelnut. “Patients are generally more generous.” The workforce is more irritated when people don’t use the equipment intended for stool samples. Bioscientia specialist Daniela Şaşma says that some samples come in jam jars. “They have replaced the film canisters. We often got them until digital photography became established.”