Data Hunters: bridging bioinformatics education and microbiome research

Abstract

Vast sequencing data in public repositories offer researchers unprecedented opportunities for gaining insights through reanalysis and machine learning approaches, thereby advancing the microbiology field. However, the lack of standardized metadata poses a significant obstacle to big data reuse, necessitating advanced bioinformatics skills for curation and integration. To tackle this challenge, we organized the Data Hunters Workshop, enabling extensive human skin microbiome metadata curation through student community engagement. The Data Hunters Workshop constitutes a student-science initiative within the University of Milano-Bicocca, Italy. Integrating theoretical and hands-on phases, the workshops structure included a 6-hour lecture, covering metagenomics and metadata manipulation fundamentals, followed by an interactive practical phase designed as a learn-and-play activity. This phase was supported by in-house developed educational online and command-line resources, facilitating students acquisition of Python commands for managing microbiome metadata. Upon the workshops conclusion, its effectiveness was assessed through surveys and standardized evaluation scales. Twenty-nine students addressed the critical challenge of metagenomics metadata standardization. Workshops resources have equipped students with foundational knowledge in metagenomics and Python programming, empowering them to curate metadata from 379 amplicon-based and shotgun sequencing projects of the human skin microbiome. The collaborative endeavors of these students will ensure the construction of a curated metadata collection. The Data Hunters Workshop established a reusable model for similar educational aims, facilitating metagenomics and bioinformatics teaching and metadata curation. It bridged education and microbiome research by focusing on human skin microbiome metadata curation, ultimately striving to construct a specific collection promptly accessible to researchers.