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DNA extracted from feces (human and bovine) and water samples was used for the massive pyrosequencing of the hypervariable V3 region of the 16S rRNA gene, revealing 4296 operational taxonomic units (OTUs). The greatest diversity was observed in samples of cattle feces, and the smallest diversity was found in a pristine water sample. Firmicutes was the predominant group in samples of human feces, while in bovine feces the dominant groups were Firmicutes and Bacteroidetes. The interaction network showed that the stool samples had the greatest diversity and, among the water samples, the one with human pollution source had the highest diversity. The LEfSe method was used to identify host biomarkers. Actinobacteria, Betaproteobacteria, and Firmicutes were identified as human biomarkers, while for cattle, the potential markers were Bacteroidetes, Tenericutes, and Spirochaetes. Host-specific markers were identified, but were not found in the water samples, suggesting either that the tools used did not have the resolution to identify markers in environmental samples, or that the contamination in the water bodies was mixed. Additionally, as the host-specific markers were isolated from non-autochthonous microorganisms, they could be affected by adverse environmental effects including physical-chemical factors and competition with native organisms.