Multi-omics analyses from a single sample: Prior metabolite extraction does not alter the prokaryotic community characterization in a diversity of sample types

In order to investigate whether it is possible to use a single sample to perform both metabolomic and prokaryotic community analyses without affecting results from the latter, the aim of this study is to test if prior metabolite extraction modifies the recovered image of community compositions. For this, we analyzed community compositions using a standard 16S rRNA high-throughput sequencing approach on two types of extractions: classical DNA extraction using a kit, or standard methanol metabolite extraction followed by the same classical DNA extraction. Communities structure and compositions were compared after the two types of extraction on different types of samples that are commonly analyzed, some coming from lab settings (non-axenic cyanobacterial strains and gut of lab-reared fish) and some from the environment (lake water, biofilm, and gut of a wild fish). To our knowledge, this study is the first attempt to test whether single sample metabolite followed by DNA extraction introduces a bias in the obtained image of prokaryotic communities.