The Human Microbiome Data Discovery short course is a week-long program, designed to increase use of data from the Common Fund Data Ecosystem (CFDE) by building data discovery and data science skills for early-stage investigators interested in human microbiome research. Needs assessment findings revealed wide variation in trainee data science preparation, alongside shared barriers in microbiome data interpretation, computational troubleshooting, metadata harmonization, and public data reuse. These findings reinforced the need for an accessible, reproducible, skill-focused training model that bridges conceptual understanding and technical execution while supporting early-stage investigators with diverse prior computational and microbiome experience.