Detailed protein activity maps assess gut health

If the organs in our bodies could talk, the intestines might reveal the most hidden truths about our lifestyle and health. Along the way, their “confessions” could provide crucial information for biomedical and clinical research. Researchers at the Weizmann Institute of Science have now given exactly this kind of ‘voice’ to the intestine.

In a study environment published in Cellthe scientists present a method that can simultaneously identify, by testing a stool sample, all proteins in the gut – including those from food, from the person’s own body and from the gut microbiome. The method therefore makes it possible to decode the interactions between these proteins with unprecedented accuracy and resolution.

The microbiome was the starting point for the research, co-led by Drs. Rafael Valdés-Mas, Avner Leshem and Danping Zheng from the laboratory of Prof. Eran Elinav, in collaboration with Dr. Alon Savidor from the Nancy and Stephen Grand Israel National Center for Personalized Medicine.

“We wanted to go beyond DNA sequencing, the usual method to study the microbiome,” says Elinav from Weizmann’s Department of Systems Immunology. “DNA can tell us which bacteria are present in the intestines and indicate their potential activity. Bacterial proteins, on the other hand, can directly reveal whether these bacteria are active, what activity they perform, and how their function affects the human body in health and disease. .”

Identifying proteins is challenging due to their sheer abundance, compounded by similarities between proteins from different species. For example, the approximately twenty thousand protein-producing genes in the human genome give rise to millions of protein variations; identifying them using existing protein databases can be complicated and very time-consuming. The Weizmann Institute’s new method addresses this challenge, in part by combining DNA sequencing and mass spectrometry to generate a smaller, patient-tailored protein map.

The method, called IPHOMED – an abbreviation of Integrated Proteo-genomics or HOst, MicrobiomE and Diet – makes it possible to decipher the entire microbiome activity by showing which proteins in a stool sample come from which bacterial strains and in what quantities. Furthermore, it identifies the proteins secreted by the human intestines in response to signals originating from the microbiome. Taken together, proteins from these two sources generate an atlas of the body’s communication with the microbiome, for example during exposure to disease-causing bacteria or to antibiotics.

Using the method, Weizmann researchers discovered that the human intestine can secrete dozens of previously unknown antimicrobial peptides that act like natural antibiotics, killing some of the bacteria in the microbiome and ultimately shaping its composition. This finding could help explain why the composition of each person’s microbiome is unique, leading to differences in disease susceptibility.

No more diet cheating

When the researchers thought they had finished developing the method, it could identify 97% of the proteins in each stool sample, which was a high percentage, but the inability to consistently characterize the remaining 3% seemed puzzling. Further research made it clear that these originated neither from the microbiome nor from body tissues: they came from food.

This revelation suggested that the Weizmann Method could potentially meet a serious, long-standing need of nutritional science, namely to provide a non-invasive way to reveal the exact details of a person’s diet. To address this challenge, the team created a database of proteins found in hundreds of food products and identified the proteins unique to each food product. These developments made it possible to learn with unprecedented precision what people had eaten from stool samples.

For example, when the method was applied to samples collected from two groups of healthy volunteers, one in Germany and the other in Israel, the method identified similar levels of wheat consumption in both populations, but only the German samples contained high amounts of pork protein ; In contrast, most of the meat proteins in the Israeli samples came from poultry.

In one of the experiments conducted by the team, volunteers were asked to consume a varying repertoire of food items, including peanuts, on certain days. The method not only accurately determined when these food items were eaten, but was also so sensitive that it could indicate consumption of as little as five peanuts per day.

In another experiment, the researchers were able to accurately monitor changes in the diet of people with gastrointestinal diseases. In one case, the method correctly identified a child with newly diagnosed celiac disease who had failed to follow his prescribed gluten-free diet.

“Our method could be used to determine whether someone keeps kosher or whether someone is as strict a vegetarian as he or she claims to be,” Elinav says with a smile.

“But on a more serious note, the traditional method of diet tracking, self-reporting, is notoriously inaccurate. Knowing with greater precision and detail what people eat, even if their meal is complex and includes multiple ingredients, can help identify which of the many components of a meal are beneficial to health and which are problematic.”

Promoting the diagnosis and treatment of diseases

To investigate the use of their new method in the diagnosis and treatment of disease, the scientists applied it to stool samples from patients with inflammatory bowel disease, which is characterized by severe intestinal inflammation that is influenced by diet and microbiome. The analysis of samples from Israeli, German and American study participants made it possible to decode in great molecular detail the altered interactions between the human gut and intestinal microbiome that lie at the origin of this disease.

The study led to the discovery of dozens of new proteins that could serve as potential future drug targets to treat this currently incurable disease. The researchers also identified human and bacterial proteins that, used together, could be developed into new biomarkers for diagnosing the type of disease, assessing its severity and monitoring its progression. These new probes promise to outperform calprotectin, the only clinically approved biomarker for inflammatory bowel disease.

Furthermore, using an IPHOMED analysis of the patients’ diets, the researchers were able to quantify the patients’ adherence to nutritional therapies for intestinal diseases and link the degree of their adherence to such diets to better inflammation control.

Furthermore, they managed to apply their non-invasive method to detect diseases in the small intestine, the long, thin tube that absorbs most protein from food in healthy people. Because the small intestine is notoriously difficult to visualize and access, this disease could not have been picked up by conventional means.

“All together, the proteins in the intestines are the ‘words’ that will one day allow us to hear exactly what our intestines are telling us and thus learn to give them exactly the help they need,” says Elinav.

“This capability will help researchers devise personalized nutritional and medical interventions for a wide range of conditions, especially those influenced by the microbiome, including inflammatory, metabolic, malignant and neurodegenerative diseases.”