Towards standardized and defendable –omics pipelines in trace organic contaminant biotransformation research with complex natural communities.
Meta-omics approaches are increasingly used in the context of contaminant biotransformation research in complex environmental communities. However, hardly any standardized procedures or recommendations exist for any step of this pipeline. In this working group, we intend to discuss the challenges, needs and possible solutions for each step along a classical meta-omics pipeline. The goals of this group are to discuss and compare currently applied methods in the omic field, identify key areas of overlap, and push towards standardization and unification of lab-bench and computational based protocols. Focus will be placed on genomic and transcriptomic applications. Specific topics will include sample collection, handling and storage, sample extraction and purification, library preparation methods, massively parallel sequencing technologies, assembly-free and assembly-based annotation methods, available public databases and data normalization. We will also specifically discuss how each of these steps depends on the different types of matrices analyzed, which may introduce a number of specific challenges (e.g., low cell densities, large eukaryotic contributions, matrix interference etc.).