Culturable Fungi Recovered from Fecal Samples of Hospitalized Patients with Nosocomial Diarrhea: Isolation, Phenotypic Characterization, and Metabolomic Profiling

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Fungi recovered from human fecal samples represent an understudied component of the gastrointestinal microbiome, yet fungi can play important roles in health and disease, particularly in hospitalized and immunocompromised patients. Here, we report the culture-based characterization of fungi isolated from fecal samples of 39 hospitalized patients with nosocomial diarrhea in Mexico City. Fungal growth was observed in approximately 40% of samples, yielding 26 isolates: 20 yeasts and 6 filamentous fungi. The predominant genera were Candida (mainly C. albicans) and Rhodotorula, with less common species including Nakaseomyces glabratus, Lodderomyces elongisporus, and yeasts previously explored for probiotic applications, Meyerozyma and Metschnikowia spp. Among filamentous fungi, Paecilomyces variotii and multiple Penicillium species were identified. Phenotypic assays demonstrated that several yeast isolates tolerated gut-associated stress conditions, including elevated temperature, bile salts, and oxidative stress, while thermotolerant filamentous fungi remained viable at temperatures up to 42°C. Cell-free supernatants and organic extracts of selected thermotolerant filamentous fungi showed moderate cytotoxic activity against non-differentiated Caco-2 cells.

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