Gut microbiome profile to the level species in diarrheic protozoan-carrier patients in Italy

The human gastrointestinal microbiota contains a diverse consortium of microbes, including bacteria, protozoa, viruses, and fungi that are involved in many physiological and metabolic as well pathogenetic processes. However, microbiological research is dominated by studies describing the impact of prokaryotic bacteria on gut microbiome with a limited understanding of their relationship with other integral microbiota constituents as protozoa. Here, we investigated the gut microbiome composition using Oxford Nanopore Technology approach in relation to protozoan colonization of Giardia duodenalis, Cryptosporidium parvum, Blastocystis sp. and Dientamoeba fragilis in patients with diarrheal diseases in Italy, taking into consideration different risk factors as protozoan coinfection, Blastocystis-subtypes, gender, age classes, origin, eosinophilia level and positivity to SARS-CoV-2 infection. Overall, out of 1413 investigated patients, 123 (8.7 %) have found positive to one or more protozoan microorganisms with a prevalence statistically significant in individuals from Northern Africa (p < 0.0001) and in the age classes 40-59 years-old (p < 0.0022). Within the 57 individuals eligible for gut microbiome analysis, diverse profiles are observed but interestingly, a predominance of the emergent Escherichia fergusonii ATCC 35469, was found across the different risk factors. Our results emphasize the importance of studies to investigate these aspects of protozoa colonization that will undoubtedly increase our understanding of complex interactions between intestinal protozoa, other microbiota organisms, and the human host.