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

Published: 27 February 2024| Version 1 | DOI: 10.17632/kh4z9ym6vf.1
Contributor:
Francesca De Filippis

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.

Institutions

Universita degli Studi di Napoli Federico II

Categories

Genomics, Metagenomics

Funding

Ministero della Salute

GR-2016-02362975

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