Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis

Antibiotic-induced gut microbiome dysbiosis (AID) is known to be influencedby host dietary composition. However, how and when diet modulates gut dysbiosisremains poorly characterized. Thus, here, we utilize a multi-omics approach to characterizehow a diet supplemented with oats, a rich source of microbiota-accessible carbohydrates,or dextrose impacts amoxicillin-induced changes to gut microbiome structure and transcriptionalactivity. We demonstrate that oat administration during amoxicillin challengeprovides greater protection from AID than the always oats or recovery oats diet groups.In particular, the group in which oats were provided at the time of antibiotic exposureinduced the greatest protection against AID while the other oat diets saw greater effectsafter amoxicillin challenge. The oat diets likewise reduced amoxicillin-driven eliminationof Firmicutes compared to the dextrose diet. Functionally, gut communities fed dextrosewere carbohydrate starved and favored respiratory metabolism and consequent metabolicstress management while oat-fed communities shifted their metabolic profile andemphasized antibiotic stress management. The metabolic trends were exemplified whenassessing transcriptional activity of the following two common gut commensal bacteria:Akkermansia muciniphila and Bacteroides thetaiotaomicron. These findings demonstratethat while host diet is important in shaping how antibiotics effect the gut microbiomecomposition and function, diet timing may play an even greater role in dietary intervention-based therapeutics.