MAGs from human gut of subjects exposed to different levels of pollution

Description

MAGs reconstructed from human gut of subjects exposed to different levels of pollution

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Contigs (>1000 bp) were also binned using MetaBAT2 v. 2.12.1, and Metagenome Assembled Genomes (MAG) quality was estimated with CheckM v. 1.1.3. Only MAGs with >50% completeness and <5% contamination were retained for further analyses. MAGs binned in this study were clustered to a genomic database including high-quality MAGs previously reconstructed from human metagenomes and NCBI RefSeq genomes using PhyloPhlAn3.0. Pairwise genetic distances between genomes were calculated using Mash (version 2.0; option “-s 10000” for sketching;). A Mash distance <5% from any of the database genomes was considered to place the MAG within the relative Species-level Genome Bin (SGB). When a MAG showed > 5% distance from any reference genomes, it was considered a novel species (unknown SGB, uSGB), and the taxonomic assignment was made at genus (> 5% and < 15% distance), family (> 15% and < 25% distance) or phylum (> 25% distance), using thresholds previously reported. RAxML 8.0 was used to generate a phylogenetic tree, including one MAG for each SGB, which was visualized in iTOL v. 5.5.1.

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