Standardized Workflow for Human Fecal Sample Collection and Automated Deoxyribonucleic Acid Extraction Using a Magnetic Particle Processor.

Gut microbiome sequencing has become an important approach for investigating microbial community dynamics in healthy and diseased states. Alterations in microbial composition have been associated with several lifestyle- and age-related disorders, including diabetes, leukemia, and neurodegenerative diseases. Because different microorganisms exhibit distinct physiological characteristics and environmental requirements, standardized fecal sample collection, transport, and processing are essential to preserve sample integrity and minimize technical variability. Variations introduced during pre-analytical handling and deoxyribonucleic acid (DNA) extraction can influence downstream microbiome analyses and affect data interpretation. The goal of this protocol is to provide a standardized workflow for human fecal sample collection and automated DNA extraction using the MagMAX Microbiome Ultra Nucleic Acid Isolation Kit (nucleic acid extraction kit) and the KingFisher Flex System (automated magnetic particle processor). The workflow integrates controlled sample handling with automated nucleic acid extraction to reduce manual variability and improve procedural consistency. The protocol includes standardized fecal sample collection, storage, preparation, automated extraction, and nucleic acid recovery from complex fecal matrices. Representative results demonstrate successful recovery of DNA suitable for downstream applications, including 16S ribosomal ribonucleic acid (rRNA) gene sequencing and shotgun metagenomic sequencing. The standardized workflow supports reproducible sample processing, facilitates scalability for microbiome studies, and promotes greater consistency across experiments. The visual demonstration provides practical guidance for implementing standardized fecal sample processing and automated nucleic acid extraction for gut microbiome research.