Next-generation sequencing is a key technology at SNIPR Biome. Having a flexible and scalable in-house sequencing pipeline with quick turnover has been a game changer in advancing our research pipeline. The workflow we developed is fully traced in our LIMS system (Benchling) and all wet lab processes are automated on our liquid handler (Hamilton STAR) to ensure a hands-off workflow with high traceability and reproducibility. Sequencing data (Illumina MiSeq) is automatically uploaded to our cloud environment (Amazon AWS) and processed in customized bioinformatics pipelines. Results are captured in our in-house developed genome portal and full traceability is maintained by using identifiers shared with our LIMS system. To exemplify how sequencing has allowed SNIPR Biome to solve complex research questions we will present a case study of combining whole genome and shotgun metagenomics sequencing to quantify low-abundant E. coli strains longitudinally in human subjects.