Meta-omics approach as a tool to investigate patients suffering from low-grade inflammatory pathologies

Based on the crucial role exerted by complex microbial communities on human health in intestinal niches and, considering the microbiota impact in related pathologies, a coordinated and massive effort is required to collect and analyse samples from stratified and diversified patient cohorts. Delving the microbiota involvement in low-grade inflammatory pathologies, we retrieved our samples from the first Italian biobank (based on the BIOMIS project) collecting saliva, stools, vaginal derivatives, blood, and serum. The biobank includes various noncommunicable diseases (NCDs) and from this whole set we picked fecal samples relative to low-grade inflammatory pathologies i.e., chronic kidney disease, type 1 and type 2 diabetes together with healthy control subjects. The samples were then used for metabolomics and metaproteomics analyses. Better detailing, metabolomics profiles were obtained by using a gas chromatograph coupled with a mass spectrometer and analysed with the NIST library. High-resolution metaproteomics sample spectra produced with an Orbitrap mass spectrometer were processed through the usage of the dedicated bioinformatics Trans-Proteomic Pipeline, TPP version 6.2.0 developed by the Seattle Proteome center and run on server Linux server provided with an Apache web server. Within the configured tools, starting from spectral data, the Comet software modules (https://comet- ms.sourceforge.net/), granted the relative quantification of peptides and proteins by comparing the resulted hits against an ad hoc customized sequence database. Python scripts have been used to extract protein entries and to create a non-redundant (https://github.com/pwilmart/fasta_utilities) UniProt database (Swiss-Prot + TrEMBL) provided together with its decoy section, useful for FDR computing. Omics data in sample groups were compared and only statistically significant hits were kept. The evaluation of metabolomics and metaproteomics results allows for depicting a complete framework of possible markers made of metabolite and protein panels in low-grade inflammatory pathologies.