Activated sludge metagenome Raw sequence reads

Candidiasis is a common hospital-acquired infection, which, when systemic, can be fatal. It is caused by Candida species and is associated with the uncontrolled outgrowth of this species in the endogenous microbiome. Hence, while most Candida species exist as harmless commensals in the gastrointestinal tract, they can transition to pathogens. This transition is associated with both a deficient immune system and an impaired gut microbiome. Currently, in vitro models allowing to mechanistically study the interaction between Candida and the gut microbiome are lacking. Hence, identifying the key microbial actors that prevent Candida outgrowth remains challenging. The significance of our research is in using the multi-compartmental semi-dynamic SHIME model to elucidate the spatial and temporal colonization kinetics of specific Candida species, including C. albicans, C. tropicalis, C. glabrata, and C. parapsilosis, under conditions of eubiosis and dysbiosis. It sets the stage for discovering factors contributing to Candida outgrowth and commensal-to-pathogen transition.