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.
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:
- Main directory: contains the Snakemake workflow files and R-scripts
scripts
subdirectory: contains auxiliary scripts utilized in the workflowenvs
subdirectory: holds the specifications for conda environmentsSingularity_Containers
subdirectory: stores the Singularity container definition files
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