From Sample to Sequence

Microbiome research increasingly demands standardized, scalable workflows to process diverse sample types. To address this, the Biobank OWL at the University of Bielefeld Medical School in Germany has established an automated platform for microbial DNA isolation and sequencing, ensuring reproducibility, flexibility, and high-quality outcomes for large-scale cohort studies.

About Dr. Timm Weber:

Dr. Weber earned a Master’s degree in Life and Medical Sciences from the University of Bonn and completed his PhD in Immunology at the Max Delbrück Center for Molecular Medicine in Berlin. There, he studied the immune response to Epstein–Barr virus and contributed to advances in CRISPR/Cas9 technology. He then joined the Institute of Virology at University Hospital Cologne as a postdoctoral researcher, where he investigated the antibody response to hepatitis C virus and SARS-CoV-2 and developed antiviral monoclonal antibodies. Since 2023, he has been a Staff Scientist at Biobank Ostwestfalen-Lippe (BOWL) at Bielefeld University, a highly automated research biobank focused primarily on human samples, where he serves as lab head and oversees quality management.

About Dr. Mirkko Flecken

Mirkko Flecken is a laboratory automation specialist at Hamilton Robotics, where he focuses on developing automated workflows that improve the efficiency, reproducibility, and scalability of modern life science laboratories. With a background in protein biochemistry, he combines scientific expertise with hands-on experience in robotics, software, and laboratory automation to help researchers streamline complex experimental processes. Mirkko Flecken earned a Master’s degree in Biology from RWTH Aachen University and received his PhD in biochemistry from the Ludwig-Maximilians University Munich for his contributions to the understanding of Rubisco activation in cyanobacteria and plants in the group of F.- Ulrich Hartl at the Max Planck Institute of Biochemistry, Martinsried.

About Geerthigan Karunakaran

Geerthigan Karunakaran is an Associate for Automation Solutions at Zymo Research Europe, where he supports the implementation and optimization of automated workflows for molecular biology applications across various laboratory automation platforms. Holding an M.Sc. in Biology with a specialization in Proteomics and a focus on Molecular Biology, Bioinformatics, and Automation, he combines scientific expertise with hands-on experience to deliver efficient and reproducible solutions for complex experimental processes.

• How to implement standardized, automated workflows for microbiome DNA isolation across diverse sample matrices.
• How to leverage modular SOPs for matrix-specific adaptations while maintaining harmonized processing.
• How to apply quality control measures to ensure reproducible and reliable microbiome data.
• How to integrate seamlessly with NGS workflows to support scalable microbiome research in large longitudinal cohorts.

A standardized end-to-end workflow—from primary sample to sequencing—enables robust and scalable microbiome research. This streamlined approach ensures high-quality analyses across diverse sample types while meeting the rigorous demands of large-scale cohort studies.