The human symbiotic microbiota produces various bio-active molecules having chemical and functional similarity to dietary nutrients and /or endogenous compounds. Various factors and agents cause the imbalance of host/microbial dialogue. Currently for conservation and restoration of human microbial community various probiotics and prebiotics are used. Unfortunately, probiotic effects are often short term or absent or uncertain; traditional probiotics may also have non-desirable side effects in the application. For these reasons, the search for microbial molecule modifiers of host/microbe axis is emerging, especially with regard to personal medicine. These compounds have been named metabiotics (M). M are structural components of known probiotic microorganisms and/or their metabolites and/or signaling molecules that can restoring shortages and disruption of the balance of mitochondrial, microbial or cellular LMW substances with increased health effectiveness. They have some advantages (certain chemical structure, well dosed, safety, long shelf-life) in optimizing host gene expression, epigenetic, energetic, metabolic, immune, informational, regulatory, transport, neuro-hormonal and/or behavioral responses associated with the symbiotic microbiota. M can act as independent means or as enriching additives in functional foods. Simple microbial molecules can also be used in constructing hybrid M containing multiple metabolites and structural components separately or in combination with herbal compounds. Special attention should be paid to the design of M with specific targets in the host. Further investigations will clarify what natural microbial or artificial (semi-synthetic, synthetic, hybolite) pan- or selective M may affect host functions, biochemical and signal processes.