Recently much attention is paid to investigation of the gut microbiome impact on children's mental health. The study was aimed to detect alterations in the taxonomic composition and content of bacterial genes encoding key enzymes involved in the metabolism of neuroactive compounds in the metagenomes of healthy young children and adolescents. The whole metagenome sequencing was used to obtain the metagenomic data of the faecal specimens. The bioinformatics algorithm developed and the catalogue of homologs created were used to identify the changes in abundance of bacterial genes and metagenomic signatures in the studied metagenomes. The core neurometabolic signature of the healthy children gut microbiota included the Bacteroides uniformis, Faecalibacterium prausnitzii and Lachnospiraceae bacterium species, as well as genes involved in production of acetic, propionic and butyric acids, glutamate and enzymes possessing antioxidant activity. Comparison of metagenomes in children of different age groups revealed significant (p < 0.1) changes in the average abundance for 3 bacterial genera and 18 species. The higher alpha diversity of the adolescents’ microbiota was observed both at the genus and species level. Furthermore, in the adolescents’ microbiota metagenomes the increased average relative abundances for the genes encoding enzymes involved in production of SCFAs, glutamate, tryptophan and compounds with antioxidant properties, histidine degradation and linoleic acid conjugation were observed (p < 0.1). The study results support the evidence that healthy gut microbial communities become more diverse and functional as their human hosts become older.