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In light of recent data, microorganisms should be construed as organisms that are capable of communication and collective behaviors. Microbial communication signals are involved both in interactions among microbial cells within microbial social systems, including the human body-inhabiting microconsortium, and the dialogue between the microbiota and the host organism. The microbiota inhabits various niches of the host organism, especially the gastro-intestinal (GI) tract. Microorganisms release diverse signal molecules and, in addition, specifically respond to host signals. This enables them to constantly interact with the nervous system including the brain and the immune system of the host organism. Evolutionarily conserved signals that are involved in the communication between microbiota and the host include neuroactive substances (neurochemicals) such as peptides, amine acids, biogenic amines, short-chain fatty acids, and gaseous substances. This ongoing dialogue may either stabilize the host’s physical and mental health state or, alternatively, cause serious health problems.