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.为构建各试验组羔羊的瘤胃微生物核心基因组目录，本研究针对每一组日粮饲喂的羔羊各选取4只个体，采集其瘤胃液与瘤胃颗粒样本（总计24份样本），从中提取的DNA进行鸟枪宏基因组测序。采用无PCR的TruSeq建库试剂盒构建测序文库，在Illumina HiSeq 4000的两个测序泳道上进行测序，生成2×150 bp的双端读段。羔羊样本的原始读段先采用Trimmomatic v0.36的双端模式进行质量过滤，随后将修剪后的读段组装为重叠群（contigs）。所有样本的个体组装与共组装分别采用metaSPAdes v3.13.0与MegaHIT v1.2.9完成（参考文献90）。个体组装得到的重叠群采用VAMB v3.0.2进行分箱，而共组装得到的重叠群则同时使用MetaBAT2 v2.12.1与MaxBin2 v2.2.7进行分箱。综合上述三种分箱策略，所有样本共获得1532个分箱（bins）。使用dRep v3.2.2以99%平均核苷酸一致性（ANI）对这些分箱进行二次去冗余处理，最终得到291个去冗余后的分箱，后续统称为宏基因组组装基因组（metagenome-assembled genomes, MAGs），这些MAGs的完整度均高于50%，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与KEGG数据库完成。