A trait-based approach unveils mechanisms shaping antibiotic-related microbial genetic machinery across European soils

This repository houses the source code related to the study of antibiotic synthesis and resistance genes, obtained using high-throughput sequencing to analyze environmental DNA from 658 metagenomic samples of topsoil, collected from various regions across Europe.

Materials

The foundation for the study is based on the European Commission's LUCAS Soil survey. These samples were collected across the European Union using a standardized protocol.

Distribution of sampling sites across environments:

Repository structure

• Main directory: contains the Snakemake workflow files and R-scripts
• scripts subdirectory: contains auxiliary scripts utilized in the workflow
• envs subdirectory: holds the specifications for conda environments
• Singularity_Containers subdirectory: stores the Singularity container definition files

Citation

Dulya O, Mikryukov V, Shchepkin DV, Pent M, Tamm H, Guazzini M, Panagos P, Jones A, Orgiazzi A, Marroni F, Bahram M, Tedersoo L. (2023) A trait-based approach unveils mechanisms shaping antibiotic-related microbial genetic machinery across European soils // DOI:10.5281/zenodo.10039980