https://www.alice.cnptia.embrapa.br/alice/handle/item/37 Embrapa Suínos e Aves (CNPSA) 2026-04-04T03:16:08Z https://www.alice.cnptia.embrapa.br/alice/handle/doc/1185972 Título: Shaping soil fungal communities: How swine waste treatment systems and geography drive fungal community shifts. Autoria: DIEHL, C.; BREYER, G. M.; TORRES, M. C.; WUADEN, C. R.; REBELATTO, R.; PASTORE, J.; NICOLOSO, R. da S.; DORN, M.; KICH, J. D.; SIQUEIRA, F. M. Conteúdo: The use of swine waste as an organic fertilizer is an important practice in sustainable agriculture. This study aims to evaluate the effects of two common swine waste treatment systems, Covered Lagoon Biodigesters (CLB) and Waste Stabilization Ponds (WSP), on fungal community structure in soil. Soil and waste samples were collected from swine farms across five Brazilian states, representing different geographical regions with distinct climate, soil types, and vegetation. A metagenomic approach was employed to analyze the fungal communities present in the samples. Our results revealed that fertilization with swine waste did not significantly affect the overall diversity of fungal communities, although distinct shifts in community composition were observed between fertilized and non-fertilized soils. Notably, reads assigned to Sugiyamaella lignohabitans were detected only in samples from waste stabilization ponds, suggesting that this environment may favor fungal taxa associated with lignocellulose degradation. Furthermore, the fungal genera Fusarium and Rhizophagus exhibited contrasting responses to fertilization, with Fusarium being more abundant in fertilized soils and Rhizophagus decreasing in abundance. Geographic variation in fungal community composition was also observed, correlating with the physicochemical properties of the soil. These findings indicate that, in our dataset, the waste treatment systems had little influence on the fungal diversity of waste samples, whereas soil fertilization with swine waste was associated with marked shifts in fungal community composition, particularly in terms of taxonomic structure. 2026-01-01T00:00:00Z https://www.alice.cnptia.embrapa.br/alice/handle/doc/1185915 Título: From farm to environment: the microbiome and the silent spread of antimicrobial resistance genes in soil despite manure management in swine farms. Autoria: BREYER, G. M.; TORRES, M. C.; REBELATTO, R.; WUADEN, C. R.; PASTORE, J.; LAZZAROTTI, M.; NICOLOSO, R. da S.; DORN, M.; KICH, J. D.; SIQUEIRA, F. M. Conteúdo: Abstract: The swine industry generates large amounts of organic waste containing antimicrobial residues, requiring efficient manure management to reduce environmental risks. Covered lagoon biodigesters (CLBs) and waste stabilization ponds (WSPs) are commonly used digestion systems, with digestates subsequently applied as organic fertilizers. Although these systems successfully reduce pathogenic bacteria, their effectiveness in removing antimicrobial resistance genes (ARGs) remains unclear. In this study, we compared microbiome and resistome profiles from CLB- (n = 23) and WSP-farms (n = 20) using shotgun metagenomic sequencing of raw and digested manure, as well as fertilized and non-fertilized soils. Our findings indicate that digestate application slightly shifted soil microbial communities and significantly increased bacterial diversity, suggesting the introduction of diverse manure-derived bacteria. Reads from taxonomic markers associated with clinically important pathogens, including Enterobacterales, streptococci (groups A and B), Enterococcus faecium, Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniae, and Salmonella enterica were still detected in digestates and fertilized soils, regardless of the digestion system. Moreover, DNA sequences associated with ARGs against critical antimicrobials, such as carbapenems, cephalosporins, and glycopeptides persisted. Notably, WSPs exhibited greater accumulation of some ARGs, including OXA-347 and vanG. Overall, although CLBs exerted a lower impact on soil microbial communities and resistomes compared to WSPs, neither system effectively eliminated ARGs. These findings highlight the potential for environmental dissemination of ARGs through manure fertilization and underscore the urgent transition toward more sustainable production practices, including eliminating non-therapeutic antimicrobial use in the swine industry, as well as the need for improved digestion technologies and continuous monitoring under the One Health framework. 2026-01-01T00:00:00Z https://www.alice.cnptia.embrapa.br/alice/handle/doc/1185918 Título: Genotypic and phenotypic characterization of Salmonella Typhimurium strains isolated from swine in the southern region of Brazil. Autoria: PEREIRA, G. do N.; CAMPOS, I. C.; GOMES, C. N.; VILELA, F. P.; KICH, J. D.; ALLARD, M. W.; FALCÃO, J. P. Conteúdo: Abstract: Salmonella Typhimurium has long been one of the most frequently isolated serovars in animal and human infections. Pork has been involved in the dissemination of S. Typhimurium to humans and plays an important role in the epidemiology of this infection. This study aimed to characterize genotypically and phenotypically S. Typhimurium strains isolated from swine in Brazil. The genomic relatedness among 17 of the 18 S. Typhimurium genomes was ≥ 90% according to Gegenees analysis, while ANI analysis showed ≥ 98.2% similarity across all 18 genomes, with most strains belonging to SNP cluster PDS000201117.2. Virulence factors and stress-related genes were searched at NCBI Pathogen Detection. All strains carried the iroB, iroC, sinH, asr, golS, and golT genes. Under acid stress, all strains survived after 10 min and 1 h. Under oxidative stress, 17 (94.44%) strains survived after 10 min, and 11 (61.11%) strains survived after 1 h. The invasion rates in Caco-2 cells ranged from 37.50% to 100%, and survival in the macrophage assay ranged from 37.50% to 87.50%. In conclusion, the close genetic relationship observed among the S. Typhimurium strains isolated from swine studied may suggest that a predominant subtype may have prevailed in Brazil’s swine sources. The high prevalence of some heavy metal tolerance encoding genes is alarming due to their potential to influence in the co-selection of S. Typhimurium strains resistant to antibiotics. Moreover, the presence of some virulence genes and the notable stress survival and cell invasion capacities highlighted the importance of surveillance to prevent the dissemination through food of virulent S. Typhimurium strains present in livestock to humans. 2026-01-01T00:00:00Z https://www.alice.cnptia.embrapa.br/alice/handle/doc/1185841 Título: Autogenous vaccines: an alternative approach to disease control in poultry. Autoria: HAACH, V.; SILVEIRA, K. R. D.; BASTOS, A. P. A. Conteúdo: Autogenous vaccines are increasingly used to control poultry diseases not adequately managed by licensed vaccines. Tailored to flock-specific pathogens, they can improve performance by reducing mortality and morbidity during outbreaks and lowering antimicrobial use in herds with recurrent bacterial challenges. Their value extends to variant viral agents affected by antigenic drift. Despite benefits, variability in efficacy and limited standardized safety data remain challenges for broader adoption. 2026-01-01T00:00:00Z