The last chapter of this book presents several perspectives for future research works, which deserve to be done in the field of the study of amino acid metabolism in prokaryotic and eukaryotic cells, and for the implication of such metabolism for physiological functions both in microbes and mammalian cells. From the point of view of basic research, an immense gap still needs to be filled regarding the long way of events linking synthesis of short catalytic peptides and amyloids to the formation of more and more complex biomolecules. Then, our understanding of the way these biomolecules self-organized in metabolic networks, up to the amino acid-dependent synthesis of very complex biomolecules, such as RNAs and then DNA, needs also a constant flow of novel data. In addition, to identify the species of Alphaproteobacteria and Asgard archaea, which were at the origin of the first eukaryotic cells, additional investigation regarding the genotype and phenotype of potential candidates, notably in a perspective of metabolic cooperation, should be helpful. From the point of view of applied research, we need to better understand how the metabolism of amino acids in commensal and pathogenic bacteria drives the communication between them and between bacteria and other microorganisms. This latter aspect is important in the context of the study of the determinants of the intestinal microbiota composition/metabolic activity for maintenance or recovery of gut health. Furthermore, efforts are required to explain in more depth how the amino acid-derived bacterial metabolites produced within the intestinal fluid regulate energy metabolism in both commensal and pathogenic bacteria, as well as how these compounds affect microbial growth/virulence, capacity to form biofilm, and toxin production. The mechanisms by which these amino acid-derived bacterial metabolites affect either positively or negatively gut health in different alimentary contexts represent also an important aspect of research to be done in that field. Finally, better understanding of the implication for human health of the co-metabolism of amino acids by the intestinal microbiota and the lodging host in different physiological and pathophysiological contexts needs additional experimental and clinical trials for future applications.