Autoprobiotic (indigenous) strains of Enterococcus faecium used in the correction of experimental intestinal dysbiosis, in contrast to probiotic E. faecium strain L-3, had a marked bifidogenic effect, preserved the populations of Escherichia, and inhibited the growth of Proteus, but had a relatively low antagonistic activity in relation to Klebsiella. Administration of autoprobiotics (A) and probiotic (P) led to faster disappearance of the symptoms of dyspepsia as compared with the control group of rats (C1) in which dysbiosis was not corrected. Animals from subgroup A1 were given A, whose genomes contained a large number of pathogenicity genes, including cytolysins and hyaluronidase. Investigations using the open field test identified various behavioral reactions to correction of dysbiosis. Animals of subgroup A1 showed suppression of movement and orientational-investigative activity. In the second group of rats (subgroup A2), movement and orientational-investigative activity was comparable with that in control group C2 (without induction of dysbiosis), as after use of P. These characteristics of the effects of autoprobiotic enterococci on the intestinal microbiota and the body support the existence of an intestinal microbiome–brain axis.