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.