Composição taxonômica da microbiota de fezes de bovinos de corte (bos indicus) e suas implicações sobre o ganho de peso: uma comparação entre condições de pasto e confinamento.

Abstract

This project aimed to investigate the diversity and abundance of microorganisms in the feces of Brazilian zebu cattle at two time points: during pasture-based growing and at the end of feedlot finishing, as well as their association with the average daily gain (ADG) phenotype. Fecal samples from 85 Nelore bulls were collected, macerated, and extracted for subsequent sequencing (Illumina PE250 platform). Specific primer pairs were used for the amplification of the 16S rRNA gene (v3-v4 region, metabarcoding) for Bacteria and Archaea. QIIME 2 was used for data processing and analysis. Raw sequences were clustered into Amplicon Sequence Variants (ASVs) using the DADA2 plugin, then annotated and compared. The SILVA database (version 138.1) was used for taxonomic assignment. Statistical analyses were performed to identify differences in microbial structure and diversity over time and to assess their impact on the ADG phenotype. According to the Shannon index, bacterial diversity was significantly higher during the dry-season grazing period compared to the rainy season and the feedlot period (p ≤ 0.05, Wilcoxon test). In contrast, Archaea diversity was higher during both the dry and rainy seasons compared to the feedlot period (p ≤ 0.05, Wilcoxon test). Non-metric multidimensional scaling (NMDS) analysis using Bray-Curtis distance revealed a distinct separation of samples from each period for bacteria, with the rainy season being more similar to the feedlot period. Conversely, for Archaea, beta diversity analysis showed greater clustering and similarity among samples across all three periods. The dominant phyla in the Archaea community were Euryarchaeota, Thermoplasmatota, and Halobacterota, with Euryarchaeota being the only phylum present during the feedlot period. The most abundant bacterial phyla were Firmicutes, Bacteroidota, Proteobacteria, and Actinobacteriota. Notably, there was a significant difference in the abundance of Proteobacteria and Bacteroidota between the dry season and other periods, with Bacteroidota being more abundant and Proteobacteria less abundant during the dry season. In the association analysis, six Archaea ASVs and four Bacteria ASVs were identified during the rainy season as associated with low ADG, while ten Bacteria ASVs and one Archaea ASV were associated with high ADG. In the feedlot period, eight Bacteria ASVs were associated with low ADG, whereas thirteen Bacteria ASVs and two Archaea ASVs were linked to high ADG. During the dry season, four Bacteria ASVs and one Archaea ASV were associated with low ADG, while six Bacteria ASVs and six Archaea ASVs were linked to high ADG. These results highlight the relative abundance of the most frequent taxa, aligning with the core microbiome concept, and higher alpha diversity during the dry season. The association analysis of ASVs with ADG identified Lachnospiraceae, Oscillospiraceae, and Rikenellaceae as key bacterial families, and Methanobrevibacter as the main Archaea taxon, with both positive and negative effects on the phenotype.