Educating through microbiome research: a reproducible approach

Although often unnoticed, the environmental microbiota is closely linked to the health of both the human microbiota and its host. However, its role remains largely misunderstood, especially by non-experts and students. Moreover, collecting environmental microbiota samples (EMS) is time-consuming, requires multiple replicates, standardized metadata, and costly processing and sequencing. To address these challenges, we developed the Bicocca Sampling Days (BSDs), a four-day event, one day per each season, where students collected EMS across different urbanized areas in the Milano-Bicocca district. Every event started with a lecture and demonstration, continued with sampling and metadata collection with a free data collection, management, and visualization platform and ended with a survey to assess the educational impacts with customized and standard scales. To ensure the reproducibility of this workflow, we provided ready-to-use templates for sampling campaign design, metadata protocols, checklists, and evaluation tools. Over eight hours of fieldwork, 76 students collected 2,429 samples over 29,288.74 m2. Participants demonstrated significant gains in microbiome sampling knowledge and confidence in microbiome sampling, with the largest improvements in perceived competence. To support this model’s sustainability, we launched the crowdfunding campaign Fantastic Microbes and Where to Find Them to fund EMS sequencing, a free workshop on microbiome data analysis and writing, and public outreach activities that raised awareness and connected citizens with microbiome research. In conclusion, we offer a reproducible model that integrates microbiome with citizen science, research, and education, while contributing to real-world research and fostering scientific literacy among students and the broader public.