Lamb rumen MAGs

To reconstruct a core rumen microbial genome catalogue from each experimental group of lambs, Extracted DNA from the lamb rumen fluid and particle samples from four animals in each diet group (n = 24 samples in total) was subjected to shotgun metagenomic sequencing. Libraries were prepared using PCR-free TruSeq chemistry and sequenced on two lanes of the Illumina HiSeq 4000 to generate 2 x 150 bp pair-ended reads. Raw reads from lamb samples were quality filtered using Trimmomatic v0.36 in pair-end mode before the trimmed reads were assembled into contigs. Both individual assemblies and co-assemblies of all samples were carried out metaSPAdes v3.13.0 and MegaHIT v1.2.9 90, respectively. Contigs from the single assembly were binned using VAMB v3.0.2, while the contigs from the co-assembly were binned using both MetaBAT2 v2.12.1 and MaxBin2 v2.2.7. Collectively, these three binning strategies generated 1,532 bins across all samples. These bins were re-dereplicated at 99% ANI using dRep v3.2.2, which resulted in 291 dereplicated bins, hereafter referred to as metagenome-assembled genomes (MAGs), with completeness above 50% and contamination below 25%. Function annotation carried out using dbCAN, PFAM, and KEGG, integrated in the DRAM v1.2.4 annotation tool.

为重建羔羊各实验组的核心瘤胃微生物基因组目录，本研究从每个日粮组的4只羔羊的瘤胃液及颗粒样本中提取DNA（总计24份样本），并对其开展鸟枪宏基因组测序。测序文库采用无PCR的TruSeq建库化学法制备，在Illumina HiSeq 4000的两个测序泳道上完成测序，生成2×150 bp的双端reads。羔羊样本的原始reads采用Trimmomatic v0.36在双端模式下进行质量过滤，经修剪后的reads被组装为重叠群（contigs）。分别使用metaSPAdes v3.13.0和MegaHIT v1.2.9^90对所有样本进行单独组装与共组装。使用VAMB v3.0.2对单独组装得到的重叠群进行分箱，而共组装得到的重叠群则分别采用MetaBAT2 v2.12.1与MaxBin2 v2.2.7进行分箱。三种分箱策略在全部样本中共生成1532个分箱。使用dRep v3.2.2以99%平均核苷酸一致性（ANI, Average Nucleotide Identity）对上述分箱进行去重，最终得到291个去重后的分箱，即宏基因组组装基因组（MAGs, metagenome-assembled genomes），其完整度高于50%且污染率低于25%。功能注释通过集成于DRAM v1.2.4注释工具中的dbCAN、PFAM及KEGG数据库完成。