Microprogen

New massive sequencing and mass spectrometry technologies are revolutionising the way molecular mechanisms of several diseases are understood. Additionally, they have made it possible to show that alterations in the human microbiome, known as dysbiosis, triggers many of them.  Along those lines, it has been proposed that the intestinal microbiome may play a significant role in developing irritable bowel syndrome (IBS), one of the most prevalent functional gastrointestinal disorders (with a prevalence of 7.8% in Spain), that considerably impairs patients’ quality of life and is an enormous economic burden for healthcare systems. Nevertheless, the studies aimed at the microbiome of patients affected by that disorder do not show conclusive results. On the other hand, it has been observed that some patients with IBS have been able to improve after following a low FODMAP (fermentable oligosaccharides, disaccharides and monosaccharides andpolyols) diet, while other patients barely respond to that dietetic treatment. The reasons for improvement and the discrepancies between patients’ responses to that treatment are completely unknown.

Because of that, in order to deepen knowledge of the pathogenesis of IBS, we created a multidisciplinary consortium that brings together three institutions that are very significant in the field of health research in Navarre (CUN-UNAV, CSIC-IDAB and Navarrabiomed), to carry out the MICROPROGEN project. The general goal of the project was to integrate and combine the most novel metaproteomics techniques with functional, molecular and structural studies to identify differentiating factors of peptide origin in the intestinal microbiomes of patients who are responsive and unresponsive to the low FODMAP diet. In addition to providing biomarkers for developing fast diagnosis kits, the study of those differentiating factors can contribute to understanding the molecular mechanisms involved in IBS and, consequently, creating new and better therapies.

The following specific goals were pursued to achieve the general goal:

Goal 1: Create a collection of biological samples from patients with IBS who underwent a low FODMAP diet nutritional treatment.
Nearly 50 patients participated in the study, 35 were diagnosed with IBS according to standard Roma IV clinical criteria. Fourteen control samples were also included. After following a diet low in fermentable carbohydrates, 16 patients responded to the diet. Stool and blood samples were obtained from all the patients (whether or not they responded), before and after the nutritional treatment. Consequently, it was possible to create the expected collection of biological samples to continue with the rest of the project’s goals.

Goal 2: Identify the metapeptidome secreted by the microbiome of R and NR patients to the diet treatment and prioritise the differential peptides.
Two proteins were identified that could be used as biomarkers for responsiveness to the low FODMAP diet. The levels of those surface proteins were restored in responsive IBS patients after undergoing the dietetic treatment. Nevertheless, they remained unaltered in patients who did not respond to the diet.

Goal 3: Functional and structural selection and characterisation of the peptides with potential amyloid, immunogenic or toxigenic functions.
Peptides that come from staphylococcus aureus, a species detected in microbiome samples, were detected that are structurally compatible with an HLA allele only found in patients. In an experimental way using X-ray diffraction of crystals generated with protein and peptides reproduced in the laboratory we deciphered the interactions that occur between a peptide derived from that bacteria and the molecule presenting antigens. That interaction and its molecular footprint open the doors to a possible association between this species and the genetic predisposition of the population to developing IBS.