Prospecção de biomarcadores da microbiota de Bos indicus criados à pasto para desempenho em confinamento

Abstract

Brazilian livestock farming is predominantly based on grazing in tropical pastures, with a brief feedlot period for finishing. Although animals spend most of their lives on pasture, most microbiota research has focused on feedlot systems. This study aimed to analyze the fecal microbiota of 85 young Nelore bulls at the end of two grazing periods (dry and rainy seasons) and at the end of the feedlot phase, in search of associations between microbial profiles and production traits such as residual feed intake (RFI), ribeye area (REA), backfat thickness (BFT), meat quality, and temperament. DNA was extracted from fecal samples, and the genomic region of the 16S rRNA gene was amplified. Amplicons were sequenced using Illumina next-generation sequencing (NGS) technology on the NovaSeq platform. The sequences obtained were quality-filtered and processed with the DADA2 pipeline, which generated amplicon sequence variants (ASVs) that were taxonomically assigned using the SILVA reference annotation database (v.138.1). ASVs with a minimum relative abundance of 0.001% and present in at least 20% of the animals were retained for further analysis. To investigate associations, two RFI-extreme groups (n=16; 8 high-efficiency and 8 low-efficiency animals) were selected, and ASVs were clustered based on correlation tests. ASVs belonging to the phyla Firmicutes and Bacteroidota were significantly associated with both groups across all periods, indicating that these taxa play an important role in the gut microbial community. Conversely, ASVs from Cyanobacteria and Desulfobacterota were only found in modules associated with high RFI (less efficient animals) during grazing periods, suggesting a possible diet-related influence. Based on statistical analyses using data from all 85 animals, one ASV from the genus UCG-005 was associated with low RFI (more efficient animals) during both the rainy-season grazing and feedlot periods, suggesting its potential as an early microbial marker for feed efficiency. Additionally, some ASVs were associated with both high and low RFI, indicating that different genera or species within the same microbial family may exert contrasting effects on the phenotype. The association study between fecal microbiota profiles and feed efficiency, meat quality, and temperament traits in young cattle under different production stages and systems revealed ASVs simultaneously linked to multiple traits, suggesting potential microbial-driven phenotypic correlations.