Impaired Autophagy in Intestinal Epithelial Cells Alters Gut Microbiota and Host Immune Responses

ABSTRACTEstablishing and maintaining beneficial interactions between the host and associated gut microbiota are pivotal requirements for host health. Autophagy is an important catabolic recycling pathway that degrades long-lived proteins and some organelles by lysosome to maintain cellular homeostasis. Although impaired autophagy is thought to be closely correlated with Crohn's disease (CD), the functional role of autophagy in the maintenance of gut microbiota is poorly understood. As autophagy-related 5 (Atg5) is a key gene associated with the extension of the phagophoric membrane in autophagic vesicles, we established a gut-specificAtg5knockout mouse model, and we found that the disruption of autophagic flux in the intenstinal epithelium cells dramatically altered the composition of the gut microbiota and reduced alpha diversity. Microbial function prediction indicated that the pathway allocated for infectious diseases was enriched inAtg5−/−mice. “CandidatusArthromitus” and thePasteurellaceaefamily were increased inAtg5−/−mice, whereasAkkermansia muciniphilaand theLachnospiraceaefamily were reduced. Transcriptome analysis revealed that two key inflammatory bowel disease (IBD)-related transcription factors, RORC and TBX21, of host cells were upregulated inAtg5−/−mice, thus elevating the Muc2-related immunological response. The findings suggest that intestinal autophagy plays a vital role in modulating the diversity and composition of gut microbiota.IMPORTANCEThe homeostasis of host-microbiota interactions is of great importance to host health. Previous studies demonstrated that disruption of autophagy was linked to inflammatory bowel disease. However, the interaction mechanism of gut microbiota regulated by autophagy was obscure. In an intestinal epithelium-specific autophagy-related 5 (Atg5) knockout mouse model, we observed a significant alteration and decreased diversity in the gut microbiota ofAtg5-deficient mice compared with that of wild-type mice. Although the numbers of some organisms (e.g.,Akkermansia muciniphilaand members of theLachnospiraceaefamily) associated with the control of inflammation decreased, those of proinflammationory bacteria (e.g., “CandidatusArthromitus”) and potential pathogens (thePasteurellaceaefamily) increased inAtg5−/−mice. Differential gene expression analysis revealed that two key genes,RORCandTBX21, involved in inflammatory bowel disease were upregulated inAtg5−/−mice. Our study suggests thatAtg5deficiency results in an imbalance of the host-microbe interaction and deterioration of the gut microenvironment.