Metagenome assembled genomes (MAGs)

Metagenome assembled genomes (MAGs) generated by taking raw reads from 58 samples that were quality-score filtered, trimmed, adapters removed, entropy-filtered (entropy =0.3), and PhiX reads removed with the program BBDuk v.38.84. After quality control, the data were normalized with BBNorm v.38.84 to down-sample reads found at high depths and make the sequence coverage more even within each sample. For each sample, the normalized reads were assembled independently with MEGAHIT v.1.2.9. Each assembly was then binned individually using MaxBin 2.0 v.2.2.6. The metagenomic assembled genomes (MAGs) were then de-replicated and representative MAGs were selected with the program dRep v.2.4. The quality of MAGs was assessed using CheckM v1.0.13 and those with at least 69% completion and <10% contamination were selected for further analysis. The remaining MAGs were compared to the non-redundant NCBI database using BLASTn 2.5.0+ to identify eukaryotic sequences, which were then filtered from the assemblies. RefineM v0.1.2 was also used to remove contigs by characterizing contigs that diverged from genomic properties within each MAG, such as G+C content, genome coverage, and tetranucleotide frequencies. Further screening of bins was conducted with CheckM’s SSU Finder to identify 16S rRNA genes. Genes that did not match the taxonomic identification of the bins were removed. CheckM was run again to obtain the quality and completion of the final bins.