Modular automated high-throughput isolation and phylogenetic identification of bacteria from complex microbiomes

Metagenomic analysis can generate hypotheses about microbiome interactions and function, yet mechanistic understanding is only possible through precise experimentation manipulating its microbiota composition. The high-throughput isolation of microbiome members thus represents a core resource in this field of research. Here, we present and test a culturomics pipeline based on the use of the limiting dilution method with multi-well plates, an optical plate reader, and barcoded sequencing for phylogenetic identification, and offer modularity by proposing different protocols and possibilities along the pipeline. Most importantly, we provide all scripts required for process automation using an affordable pipetting robot, along with associated estimates of financial and labor costs.