Best practices from open data science are spreading across research fields, providing new opportunities for research and education. Open data science emphasizes the view that digitalization is enabling new forms of resource sharing, collaboration and outreach. This has the potential to improve the overall transparency and efficiency of research. Microbiome bioinformatics is a rapidly developing area that can greatly benefit from this progress. The concept of microbiome data science refers to the application of best practices from open data science to microbiome bioinformatics. The increasing availability of open data and new opportunities to collaborate online are greatly facilitating the development of this field. A microbiome data science ecosystem combines experimental research data with open data processing and analysis and reproducible tutorials that can also serve as an educational resource. Here, we provide an overview of the current status of microbiome data science from a community developer perspective and propose directions for future development of the field.