It is now accepted that all eukaryotes must be considered asmeta‐organisms, forming a close and interdependent associationbetween a host and a collection of symbiotic microorganisms(microbiota) such as bacteria, archaea, smalleukaryotes, and viruses that forms an inseparable functionalunit within which pathogenicity is far from being the norm.Symbiosis refers to the close and long‐term association andbiological interactions between two species. This associationcan be mutualistic, commensal, or parasitic depending on theevolutive outcome for each partner. Functional interactions inmetaorganisms contribute to many aspects of host physiology,such as development, morphogenesis, metabolism, aging,behavior, pathogen protection and resistance, and maturationof immunity (Esser et al., 2019). Thus, interest for microbiomeshas tremendously increased over the past two decades. Themicrobiome can be considered as a proper organ containing atleast the same number of bacterial cells as host cells, andpossessing its own genome with millions of unique genes.Research on eukaryotes' microbiome originally derived fromenvironmental microbiome research, that is, microbial ecology.In this field, microbial ecotoxicology recently emerged (Pesceet al., 2020). Indeed, like any other living organism, microorganismsare affected by environmental stressors. Microbialecotoxicology studies how pollutants alter microbial activities,including inhibition and development of adaptive resistanceresponses, and eventually the consequences up to the communitylevel and the resulting effects on ecosystem health. Itis thus legitimate to wonder what consequences an imbalancein the structure or the function of the microbiome, referredto as dysbiosis, would have on fitness, susceptibility tocontaminants, metabolic disorders such as inflammatoryresponses, and etiology of diseases in the host. However, thiscomponent of the physiology of the organisms remains largelyneglected by ecotoxicologists.
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