Data set

The research inestigated the effect of sorghum-based feed on rumen archaea in goats.
Quality evaluation of the initial sequencing data was conducted using FastQC version 0.12.1, focusing on adapter contamination, GC content distribution, per-base Phred scores, and sequence duplication rates. Raw sequencing data from 16 samples exhibited satisfactory initial quality and consistent 150 bp read lengths prior to processing. Fastp v0.23.4 software was used to trim adapter sequences and perform quality-based filtration. Following Trimmomatic processing, low-quality bases (Q<20) and readings <50 bp were eliminated, retaining 85% of the raw data (8.5 million/sample). The read length distribution transitioned from a pre-trim homogeneity of 150 bp to a post-trim profile of 100–140 bp, indicating successful adaptor removal. Taxonomy classification was performed using Kraken2 v2.1.2 at a confidence level of 0.1, utilizing the Standard-64GB database (RefSeq 2023-10 release). The Kraken2/Bracken pipeline was chosen due to its use of the comprehensive, genome-based RefSeq database. This database provides better taxonomic resolution for rumen archaea compared to 16S rRNA-specific databases. Additionally, Kraken2/Bracken offers increased speed and accuracy in classifying microbial sequences within complex communities (Stewart et al., 2019). Optimal sensitivity for detecting low-abundance methanogenic species was achieved with a confidence threshold of 0.1. To reduce the possibility of false-positive results, the abundances were tweaked using Bracken v 2.8. Only taxa with a relative abundance of 0.1% or higher in one sample were kept for further analysis. This cautious filtering method has been shown to be effective in previous metagenomic research (Beaulaurier et al., 2021). Species-level abundance was re-evaluated with Bracken v2.8. The dominance of phyla and genera was visualized using Hierarchical Krona charts and Sankey diagrams (R package: ggsankey). Alpha diversity was assessed with the Shannon index based on rarefied data (using Kruskal-Wallis tests for significance. Methanogen community composition/Beta diversity was compared via Principal Coordinate Analysis (PCoA), utilizing Bray-Curtis dissimilarity.