Mechanisms ensuring homeostasis and integrity of complex microbial populations

The existence of complex (multi-species) microbial communities is more the rule than the exception in marine and terrestrial environments, as well as in microbiota associated with living organisms (plants and animals). The "new microbiology" has seized on this theme, particularly in the field of infectious diseases, where we have moved from the classic, binary concept of "one pathogen-one host" to the "ménage à trois" concept of "one pathogen-one microbiota-one host". It is essential to understand the genetic and molecular bases that govern the establishment, maintenance and resilience of these microbial societies, including the nature of the selective pressures that led to their formation. Survival within complex microbial populations comes at the price of ruthless competition for nutritional resources. This phenomenon can be interpreted in the context of an extension of Jacques Monod's equations modeling the relationship between limiting nutrient concentration and bacterial growth. This competition will eventually generate "objective alliances", symbioses and mutualisms, the logic of which remains to be deciphered: "law of the first occupant", "barrier effect". However, this competition is not exclusively nutritional in nature; it is also based on an "arms race". The mechanisms of attack and defense between microorganisms, the main elements of which are beginning to be identified, is a major theme of research, putting effectors such as bacteriophages and colicins into their true ecological perspective, and revealing complex defense and attack systems such as CRISPR-Cas and type 6 secretion apparatuses. The antibiotic resistance crisis is undoubtedly a collateral damage of this intermicrobial "arms race", fanned by the uncontrolled use of antibiotics. These recent discoveries are expected to have a huge medical impact.