So far, the organizational and scientific foundations for the project have been successfully established, including amongst others, the receipt of ethical approvals to perform the respective clinical studies and sample collections, the setup and application of detailed standard operating procedures for sample collection, optimal storage, and transport, as well as the recruitment of all study participants. Faecal, blood, urine, and saliva sample collections (baseline and longitudinal) have been completed, forming the foundations to develop robust classification and prediction methods (Objective 1, Objective 2). The immunomodulatory properties of specific microbiota have been assessed in vitro using the HuMiX gut-on-a-chip model (Objective 3). A detailed description of the clinical study protocol was published in a peer-reviewed journal, and protocols for sample processing have been developed and published. A rich set of metadata, e.g. clinical lab readouts or dietary habits, of the study participants, has been collected. The necessary wet-lab procedures for obtaining extracellular biomolecules (DNA, RNA, (poly)peptides and metabolites) from the collected microbiome samples have been established and published in a peer-reviewed journal. Our newly developed approach for absolute quantification of high-resolution meta-omics data has been applied to the respective biomolecular fractions during the extraction process to generate high-resolution meta-omics data to resolve the composition, functional potential and activity of the gut microbiome as well as the effector molecules produced. This wealth of intracellular and extracellular meta-omics data is currently being processed and integrated. Multiple manuscripts highlighting the developments and outcomes linked to the project have been published in peer-reviewed journals. These include, among others, a knowledge base (Expobiome Map) compiling the body of knowledge on interactions of microbial taxa, microbial molecules, human immune pathways, and diseases; a framework to model microbial community dynamics resolved using meta-omics data and enabling robust predictions of up to three years into the future, and in vivo results revealing how diet and bacterial curli (a protein cross-seeding with α-Synuclein) exacerbate motor performance, as well as intestinal and brain pathologies in a mouse model of Parkinson’s disease. Moreover, a depletion of a specific B cell population was identified in individuals with rheumatoid arthritis compared to healthy controls. Several preprints presenting the most recent research outcomes have been deposited, which are currently undergoing review in peer-reviewed journals. These include an updated software tool for the prediction of antimicrobial resistance genes, virulence factors, toxins, and biosynthetic gene clusters (PathoFact 2.0); and the identification of altered microbial taxonomy, function, and expression in PD.
