Importance of amoebae as a tool to isolate amoeba‐resisting microorganisms and for their ecology and evolution: the <scp><i>C</i></scp><i>hlamydia</i> paradigm

<jats:title>Summary</jats:title><jats:p>Free‐living amoebae are distributed worldwide and are frequently in contact with humans and animals. As cysts, they can survive in very harsh conditions and resist biocides and most disinfection procedures. Several microorganisms, called amoeba‐resisting microorganisms (<jats:styled-content style="fixed-case">ARMs</jats:styled-content>), have evolved to survive and multiply within these protozoa. Among them are many important pathogens, such as <jats:italic>Legionella</jats:italic> and <jats:italic>Mycobacteria</jats:italic>, and also several newly discovered <jats:styled-content style="fixed-case"><jats:italic>C</jats:italic></jats:styled-content><jats:italic>hlamydia</jats:italic>‐related bacteria, such as <jats:styled-content style="fixed-case"><jats:italic>P</jats:italic></jats:styled-content><jats:italic>arachlamydia acanthamoebae</jats:italic>, <jats:styled-content style="fixed-case"><jats:italic>E</jats:italic></jats:styled-content><jats:italic>strella lausannensis</jats:italic>, <jats:styled-content style="fixed-case"><jats:italic>S</jats:italic></jats:styled-content><jats:italic>imkania negevensis</jats:italic> or <jats:styled-content style="fixed-case"><jats:italic>W</jats:italic></jats:styled-content><jats:italic>addlia chondrophila</jats:italic> whose pathogenic role towards human or animal is strongly suspected.</jats:p><jats:p>Amoebae represent an evolutionary crib for their resistant microorganisms since they can exchange genetic material with other <jats:styled-content style="fixed-case">ARMs</jats:styled-content> and develop virulence traits that will be further used to infect other professional phagocytes. Moreover, amoebae constitute an ideal tool to isolate strict intracellular microorganisms from complex microbiota, since they will feed on other fast‐growing bacteria, such as coliforms potentially present in the investigated samples. The paradigm that <jats:styled-content style="fixed-case">ARMs</jats:styled-content> are likely resistant to macrophages, another phagocytic cell, and that they are likely virulent towards humans and animals is only partially true. Indeed, we provide examples of the <jats:styled-content style="fixed-case"><jats:italic>C</jats:italic></jats:styled-content><jats:italic>hlamydiales</jats:italic> order that challenge this assumption and suggest that the ability to multiply in protozoa does not strictly correlate with pathogenicity and that we should rather use the ability to replicate in multiple and diverse eukaryotic cells as an indirect marker of virulence towards mammals. Thus, cell‐culture‐based microbial culturomics should be used in the future to try to discover new pathogenic bacterial species.</jats:p>