The article presents QIIME 2, a new microbiome data science platform that is reproducible, interactive, scalable, and extensible. It replaces the previous QIIME 1 platform and offers improved functionality for analyzing microbiome data. QIIME 2 is built on a plugin architecture, allowing third-party contributions and supporting a wide range of tools for sequence quality control, taxonomy assignment, and phylogenetic insertion. It also includes new functionalities such as microbiome paired-sample and time-series analysis, and machine learning. QIIME 2 provides interactive visualization tools for exploratory analysis and result reporting, and allows users to securely share and interact with results without installing QIIME 2. The platform includes a decentralized data-provenance tracking system, ensuring reproducibility and transparency. QIIME 2 also supports multi-omics analysis and offers interfaces for different user types, including end-users, data scientists, and experts in high-performance computing. The platform is open-source and free for all use, including commercial, and is licensed under a BSD three-clause license. It is interoperable with other tools through plugins, file exchange in standard formats, or multi-language environments. QIIME 2 is designed to be a powerful data science platform that can be rapidly adapted to analyze diverse microbiome features. The article also discusses the differences between QIIME 2 and other microbiome data science tools such as mothur, phyloseq, and the biobakery suite. The authors highlight the benefits of QIIME 2, including its ability to support retrospective data-provenance tracking, multi-omics analysis, and interoperability with other tools. The article concludes by emphasizing the importance of QIIME 2 in advancing microbiome research and enabling accessible, community-driven microbiome data science.The article presents QIIME 2, a new microbiome data science platform that is reproducible, interactive, scalable, and extensible. It replaces the previous QIIME 1 platform and offers improved functionality for analyzing microbiome data. QIIME 2 is built on a plugin architecture, allowing third-party contributions and supporting a wide range of tools for sequence quality control, taxonomy assignment, and phylogenetic insertion. It also includes new functionalities such as microbiome paired-sample and time-series analysis, and machine learning. QIIME 2 provides interactive visualization tools for exploratory analysis and result reporting, and allows users to securely share and interact with results without installing QIIME 2. The platform includes a decentralized data-provenance tracking system, ensuring reproducibility and transparency. QIIME 2 also supports multi-omics analysis and offers interfaces for different user types, including end-users, data scientists, and experts in high-performance computing. The platform is open-source and free for all use, including commercial, and is licensed under a BSD three-clause license. It is interoperable with other tools through plugins, file exchange in standard formats, or multi-language environments. QIIME 2 is designed to be a powerful data science platform that can be rapidly adapted to analyze diverse microbiome features. The article also discusses the differences between QIIME 2 and other microbiome data science tools such as mothur, phyloseq, and the biobakery suite. The authors highlight the benefits of QIIME 2, including its ability to support retrospective data-provenance tracking, multi-omics analysis, and interoperability with other tools. The article concludes by emphasizing the importance of QIIME 2 in advancing microbiome research and enabling accessible, community-driven microbiome data science.