Human gut microbiome is highly influenced by environmental factors, the host lifestyle and the geographic region. Efforts to understand the role of the gut microbiome in cancer on a local scale are needed to incorporate this knowledge in the clinic. We recruited 25 patients (melanoma, renal cell carcinoma, non-small cell lung cancer, and head and neck squamous cell carcinoma) and we aimed to characterize the diversity of the microbiota. Using shotgun metagenomics and culture-based tools we profiled the microbial composition of our uruguayan cohort. We compared the taxonomic diversity, gene families and metabolic pathways of our oncologic cohort with a healthy reference (n = 68). The microbial composition of the oncologic cohort differs from that of the healthy control. Our results show higher relative abundance of Enterococcus faecium and Klebsiella pneumoniae as compared to healthy individuals. Using culture-based techniques, we began the first Uruguayan microbial biobank from the gut microbiome.