Complex polysaccharides such as pectin are receiving increasing attention as emergent prebiotics which could be of interest for human health. Pectin comprises a wide array of highly complex and diverse polysaccharide structures, which are abundant in agricultural by-products. Pectin metabolization by the gut microbiota requires cooperative metabolism and cross-feeding networks among microbial species. Herein we have deepened into the gut modulatory properties of apple pomaces and pectins derived from this by product, through a shotgun metagenomics approach coupled to advanced functional annotation and prediction of cooperating networks of metagenome-assembled genomes (MAGs). For this purpose, we have used samples from batch in vitro fecal fermentations performed with samples from healthy donors and Crohn's disease patients, in the presence of apple pomace and pectins exhibiting different structural properties. Our results confirm the capacity of apple pomace/pectins to promote key taxa generally underrepresented in Crohn's disease patients but that have been attributed anti-inflammatory properties, Faecalibacterium, Ruminococcaceae members and Akkermansia being very remarkable. Besides, some Ruminococcus and Akkermansia species have been identified as key symbionts, exhibiting complementary metabolic traits to fully metabolise pectins from apple pomace. These results will aid developing microbiome-targeted prebiotic and/or synbiotic strategies for specific population groups.

The research performed was funded by the European Union's Horizon2020 Research and Innovation Programme under grant agreement No 818368 (MASTER), and the grants from the Spanish State Research Agency RTI2018-095021-J-I00. CS is a postdoctoral researcher supported by the Juan de la Cierva-Formación Postdoctoral Trainee Program from MICINN, the Spanish Ministry of Science and Innovation (FJC2019-042125-I). Research in our group is also supported by Grant AYUD-2021-50910 from the autonomic Government of Principado de Asturias (FICYT, supported by FEDER).