The probiotics Akkermansia muciniphyla, that exert a favorable effect on the disrupted metabolism associated with obesity, and Faecalibacterium prausnitzii, whose absence was associated with Crohn’s disease, upregulate HDAC3 and HDAC5, affect the expression of genes involved in host lipid metabolism and epigenetic activation or silencing of gene expression. Here, HDAC3 is linked to obesity due to melanocortin 4 receptor deficiency.