Micael Siegert Schimmunech^a, Carolina Deuttner Neumann Barroso^a, Anderson Ferreira Da Cunha^b, Marcelo Mendes Brandão^c, Daniel Cruz^d , Karina Ishida^d, Marcelo Beltrão Molento^a,*
^a Laboratory of Veterinary Clinical Parasitology, Department of Veterinary Medicine, Federal University of Paraná, Curitiba, PR, Brazil. This email address is being protected from spambots. You need JavaScript enabled to view it. 
^b Laboratory of Biochemistry and Applied Genetics, Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil.
^c Laboratory of Integrative and Systemic Biology, Center of Molecular Biology and Genetic Engineering, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.
^d World Animal Protection. São Paulo, SP, Brazil.

Pig farming has a significant environmental impact and generates substantial waste. Conventional wastewater treatment on farms often fails to eliminate pathogens, posing transmission risks. This study examined the microbiome of water samples (n=10) from pig farm environments (n=6) and urban areas (n=4) in Brazil. Pig farm samples were from Itambaracá, Paraná, and Chapecó, Santa Catarina, while urban samples were from Curitiba, Paraná, Joinville, and Santa Catarina. Samples included two from before (UP) and after (DOWN) pig farm presence, and two from a city river (CITY) near pig farms. Urban samples were taken from river sources (n=2) and near metropolitan perimeters (n=2). Proteobacteria dominated 90% of samples, with only one sample (P6) showing Firmicutes as predominant. Two pre-DNA extraction techniques were compared: a commercial kit and membrane vacuum filtration. The commercial kit detected E. coli in all samples and P. aeruginosa in 60%. The vacuum filtration technique found Burkholderiales (64%), Burkholderiaceae (81%), and Acidovorax (40%) to be predominant. The commercial kit showed higher Proteobacteria prevalence (>82%) and 100% Gammaproteobacteria. E. coli O157:H7 and Shigella flexneri 2a str. 301 were detected in all commercial kit samples and one vacuum filtration sample. Urban river source samples exhibited high bacterial diversity (615 genera, 736 species in P1; 640 genera, 802 species in P5) with a predominance of Alphaproteobacteria (52%). Samples from the rivers' final courses had reduced diversity (270 genera, 386 species in P2; 25 genera, 24 species in P6) and Gammaproteobacteria predominance. The comparison between the points before (UP) and after (DOWN) did not result in a noticeable correlation of influence from pig farming on the alteration of microbial composition in the samples. Our results highlight the presence of pathogenic bacteria in the aquatic environment surrounding pig farms and emphasize the potential threat to human, animal, and environmental health.