Microbioma de bovinos Purunã em diferentes sistemas de produção a pasto durante os meses quentes

Abstract

The Purunã beef cattle breed was developed in Paraná and has shown promise for regions with a humid subtropical climate. With the advancement of global warming, heat stress is a significant concern for producers, as it leads to production losses and a low level of well-being. In the intestinal environment, microorganisms interact with the host and directly affect metabolic processes during the summer season. This study aimed to evaluate the impact of different management systems (Irrigation, Silvopastoral, and Full Sun) on the bacterial composition of Purunã cattle calves. Seventy-two fecal samples were collected in three experimental periods (0, 42, and 84 days) and 26 salivary samples (at 42 days). DNA was extracted from the samples and amplified by PCR using a specific primer for the V4-V5 region of the gene encoding the 16S rRNA region. The amplicons were sequenced on the Illumina NovaSeq platform, and the raw sequences were processed using QIIME-2 software for clustering into ASVs (a total of 783 ASVs). Diversity and composition analyses were performed in MicrobiomeAnalyst. For fecal microbiota analyses over time, overall, time was the factor with the most significant impact on the bacterial community. Alpha diversity showed no statistical difference between days 0 and 42, but increased significantly on day 84 (p < 0.05) in all treatments. Beta-diversity confirmed this temporal adaptation, showing that the microbial composition on day 84 was statistically distinct from the communities on days 0 and 42 (p < 0.01). In contrast, when comparing treatments (Full Sun, Irrigation, and Silvopastoral), fecal alpha diversity showed no statistical difference (p > 0.05) between systems. However, differential abundance analyses (DESeq2) revealed distinct metabolic signatures: Full Sun favored the microorganisms Streptococcus and Olsenella, while Irrigation and Silvopastoral selected Phascolarctobacterium. Relative abundance showed temporal adaptation marked by the reversal of the Firmicutes:Bacteroidota ratio and the establishment of a mature community on day 84, indicated by the Christensenellaceae R-7 group biomarker (ISA/LEfSe). The analysis was performed using RStudio [trade mark] software (v2024.4.4.2). The study concludes that bovine microbiota is resilient to acute climatic disturbances (day 42) but adapts profoundly over time (84 days). Although management systems do not alter total diversity, irrigation and silvopastoral systems have been shown to select microorganisms that promote animal welfare, making them viable alternatives for animal production. Next, fecal samples were compared vs. saliva at 42 days. Fecal alpha-diversity was significantly higher (p < 0.05) than salivary alphadiversity, and beta-diversity showed that they are two completely distinct communities. Taxonomically, saliva was dominated by Proteobacteria, Bacteroidota, and Firmicutes, while feces were composed almost exclusively of Firmicutes and Bacteroidota. The diversity and composition of bacterial communities in bovine fecal samples proved to be dynamic and responsive to different treatments over time, and highlight the importance of implementing production systems that promote animal welfare and microbiome stability, such as the Silvipastoral system.