Amoebae are single-celled protists that are widely found in water, soil, and other natural habitats (Samba-Louaka et al., 2019;Zheng et al., 2022). They have also been found in engineered systems such as swimming pools and drinking water systems (Delafont et al., 2013;Thomas et al., 2006;Thomas & Ashbolt, 2011). Amoebae are a significant threat to human health because some of them are pathogenic and even lethal to humans (Shi et al., 2021;Thomas & Ashbolt, 2011). In addition, diverse microbes, including bacteria, fungi, and viruses, many of which are human pathogens, have been found hidden within amoebae (Shi et al., 2021;Strassmann & Shu, 2017). For example, Legionella pneumophila can reside within amoebae, using them as their replication hosts (Hoffmann et al., 2014). Moreover, recent studies suggest that amoebae are resistant to drinking water disinfection and further protect their intracellular bacteria from disinfection (He et al., 2021(He et al., , 2022. Therefore, both amoebae and their bacterial symbionts are a significant threat to public health, and a better understanding of their interactions is in urgent need.