Activated sludge metagenome Raw sequence reads

C. albicans harmless commensal of GIT in humans, but also opportunistic pathobiont in vulnerable patients. Knowledge about C. albicans mostly limited to studies using the standard reference isolate SC5314. However, large phenotypic and genotypic diversity of clinical isolates resulting in metabolic, colonization, gene expression including fungal toxin candidalysin, pathogenicity, and drug resistance variations.In particular, C. albicans SC5314 cannot colonize the WT murine gut unless mice were subjected to antibiotic treatments or have immature microbiome. Contrastingly, isolates like 529L and CHN1 colonize the GI tract in absence of antibiotic supplementation. In addition, 101 elicits a delayed and weaker immune response compared to SC5314 which allow it to persist in the oral mucosa. Hence, SC5314 might not be the archetype strain for studying C. albicans in commensalism. It also highlights strain heterogeneity in colonization potential. Recent reports highlighted the presence of genetically distinct and phenotypically diverse C. albicans strains co-existing in healthy individuals. However, the impacts of strain heterogeneity co-occurring within the host on pathogenicity, host responses, C. albicans-microbiome interactions, and niche specificity are unknown. Hence, in our study, we used the highly controlled in vitro technology SHIME, recently validated to study fungal, and especially C. albicans-microbiome interactions. This system is devoid of host-microbiome component, thus enabling us to study solely from an ecological standpoint the inter-C. albicans strains interactions, when different strains co-exist, and C. albicans-microbiome interactions. We performed the experiments in microbe-free or in presence of microbiome background, with or without co-occurence of strains SC5314 and 101, and simulating the human proximal colon. Overall, our work highlights strain competition and fitness differences.