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Social stress can promote a variety of neuropsychiatric illnesses, many of which have a high co-morbidity with gastrointestinal disorders. Recent data indicate that gastrointestinal microbiota can affect their host’s brain and behavior. Syrian hamsters are ideal subjects for social stress research because they are territorial, aggressive, and rapidly form dominant/subordinate relationships. The purpose of this study was to determine if exposure to social stress in hamsters alters gut microbiota in dominants and subordinates after an agonistic encounter and if pre-stress gut microbiota composition is correlated with the outcome of such a conflict. Microbiota composition was assessed via 16S mRNA Illumina sequencing on fecal samples. One agonistic encounter caused a decrease in alpha diversity in both dominant and subordinate animals with a more pronounced decrease after repeated encounters. PERMANOVA analysis of the unweighted unifrac distance revealed a distinct change in beta diversity after one and nine encounters in both dominants and subordinates. Linear discriminant analysis (LEfSE) showed bacteria from the order Lactobacillales were significantly reduced following social stress in both dominants and subordinates, and both groups exhibited increases in phyla Bacteroidetes and decreases in phyla Firmicutes following repeated encounters. LEfSE analysis on samples collected prior to social interaction revealed that some microbial taxa were correlated with a hamster achieving dominant or subordinate status. These data suggest that even an acute exposure to social stress can impact gastrointestinal microbiota and that the state of the microbial community before social stress may predict dominant/subordinate status following a subsequent agonistic encounter.