Introduction: Parasitosis is an infectious disease that puts the life of patients at risk, with higher prevalence in vulnerable groups, such as the infant population. Objective: For this reason, the present research aims to indicate the influence of parasites in the intestinal microbiota of Ecuadorian infants. Methods: The sample population consisted of 264 boys and girls, aged 5 to 10 years, belonging to rural communities of Chimborazo, Ecuador. Stool samples were collected for analysis by the coproparasitic examination technique, and for confirmation of results, 8% of the total samples were analyzed by the Willis flotation concentration method. For the determination of microbiota, massively parallel NGS sequencing was performed, and statistical analysis was performed by chi-square to determine risk factors.Results: The prevalence of parasitosis in children was 44.32%, the most prevalent species being: Entamoeba coli (58.86%), Entamoeba histolytica (17.72%), and Giardia lamblia (10.13%). The presence of Trichuris trichiura eggs was identified by the Willis flotation method. The risk factors for intestinal parasitosis in the study population were: contact with pets, decay in the sanitary service infrastructure, lack of hygienic habits and garbage collection. The most prevalent bacterial population of the intestinal microbiota are: Prevotellaceae (55%), Proteobacteria (47%), Firmicutes (27%), and Treponema (17%). Conclusion: There is a significant relationship between predisposing factors and intestinal parasitosis, and it directly affects intestinal symbiosis.
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