The intestinal microbiome has been extensively studied; however, the viral component has been poorly characterized despite its crucial role in intestinal homeostasis. This study analyzed the intestinal virome of human fecal samples (n=37) from patients in Intensive Care Units (ICU) (n=10), patients hospitalized in non-ICU settings (n=13), and healthy community individuals (n=14), using sequencing by Oxford Nanopore Technologies (ONT) and Illumina. On average, 161,855 reads per sample were obtained using ONT sequencing, of which approximately 0.03% corresponded to viral reads. For Illumina, around 20,286,589 reads per sample were obtained, of which approximately 0.1% were assigned to viruses. Bacteriophages of the order Caudovirales, including Myoviridae, Podoviridae, and Siphoviridae, were identified as the main viral families. Although most viral families remained stable, a significant decrease in Microviridae was observed in hospitalized and ICU patients, suggesting an imbalance associated with the intrahospital environment. Of the prophages detected in Assembled Genomes from Bacterial Metagenomes (MAGs), the presence of two viral families (Myoviridae and Siphoviridae) in the same bacterial species, Alistipes putredinis, was noteworthy. The results suggest that bacteria-phage interactions may not always be species- specific, highlighting the complexity of microbial interactions in the human intestine. These findings represent a baseline for understanding the influence of an intrahospital environment on the composition of the intestinal virome. Further research is needed to fully understand how these changes may affect host health, especially in clinical settings.
