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

posted on 2024-06-11, 07:05 authored by Brown University
Antibiotic-induced gut microbiome dysbiosis (AID) is known to be influenced by host dietary composition. However, how and when diet modulates gut dysbiosis remains poorly characterized. Thus, here we utilize a multi-omics approach to characterize how a diet supplemented with oats, a rich source of microbiota-accessible carbohydrates, or dextrose impacts amoxicillin-induced changes to gut microbiome structure and transcriptional activity. We demonstrate that oat administration during amoxicillin challenge provides 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 exposure induced the greatest protection against AID while the other oat diets saw greater effects after amoxicillin challenge. The oat diets likewise reduced amoxicillin-driven elimination of Firmicutes compared to the dextrose diet. Functionally, gut communities fed dextrose were carbohydrate starved and favored respiratory metabolism and consequent metabolic stress management while oat fed communities shifted their metabolic profile and emphasized antibiotic stress management. The metabolic trends were exemplified when assessing transcriptional activity of two common gut commensal bacteria: Akkermansia muciniphila and Bacteroides thetaiotaomicron. These findings demonstrate that while host diet is important in shaping how antibiotics effect the gut microbiome composition and function, diet timing may play an even greater role in dietary intervention-based therapeutics.


National Institute of Food and Agriculture, 1023111

Division Of Graduate Education, 1644760

National Institute of Diabetes and Digestive and Kidney Diseases, R01 DK125382


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BioProject Curation Staff


National Center for Biotechnology Information

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  • Non-geospatial

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  • biota

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sequence analysis

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  • No

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  • Public

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It is recommended to cite the accession numbers that are assigned to data submissions, e.g. the GenBank, WGS or SRA accession numbers. If individual BioProjects need to be referenced, state that "The data have been deposited with links to BioProject accession number PRJNA991569 in the NCBI BioProject database ("

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