Dysfunction of the gut microbiota in Crohn's disease

Background: Crohn's disease (CD) results from alterations in gut microbiota and the immune system. However, the precise metabolic dysfunctions of the gut microbiota during CD is still unclear. Here, we investigated the metagenome functions using PICRUSt2 during CD course for better understanding microbiota-related disease mechanisms in order to provide new insight for novel therapeutic strategies.Results: A total of 567 stool samples collected from 383 CD patients provided total data for 291 remission (CR), 177 mild-moderate (CM) and 99 severe disease status (CS). As expected, changes in alpha and beta diversity, in networks and increase in Proteobacteria abundance were associated with disease severity. However, microbial function was notably more consistently graduated disturbed than composition from CR, to CM and then to CS. Major shifts in oxidative stress pathways, as well as decreased carbohydrate, aminoacid metabolism in favor of nutrient transport were identified in CS compared to CR. Increases in virulence factors were also notable to invade the host, to evade the host defenses and to participate in the establishment of the inflammation.Conclusions: This inferred functional metagenomic information provides new insights into community-wide microbial processes and pathways linked to CD pathogenesis. This study paves the way for new advanced strategies to rebalance gut microbiota and/or eliminate oxidative stress, biofilm to down regulate the gut inflammation.