Domestication of animals can lead to profound phenotypic modificationswithin short evolutionary time periods, and for many species behavioralselection is likely at the forefront of this process. Animal studies have stronglyimplicated that the gut microbiome plays a major role in host behavior andcognition through the microbiome–gut–brain axis. Consequently, herein, it ishypothesized that host gut microbiota may be one of the earliest phenotypesto change as wild animals were domesticated. Here, the gut microbiomecommunity in two selected lines of red junglefowl that are selected for eitherhigh or low fear of humans up to eight generations is examined. Microbiotaprofiles reveal taxonomic differences in gut bacteria known to produceneuroactive compounds between the two selection lines. Gut–brain moduleanalysis by means of genome-resolved metagenomics identifies enrichmentin the microbial synthesis and degradation potential of metabolites associatedwith fear extinction and reduces anxiety-like behaviors in low fear fowls. Incontrast, high fear fowls are enriched in gut–brain modules from the butyrateand glutamate pathways, metabolites associated with fear conditioning.Overall, the results identify differences in the composition and functionalpotential of the gut microbiota across selection lines that may provideinsights into the mechanistic explanations of the domestication process.