QIIME is an open-source software pipeline for analyzing high-throughput microbial community sequencing data. It was developed to address the challenges of handling large datasets generated by high-throughput sequencing technologies, such as pyrosequencing with error-correcting barcodes. QIIME is built using the PyCogent toolkit and supports a wide range of microbial community analyses, including network analysis, diversity histograms, and identification of core microbial communities. It provides graphical displays for data interaction and is highly modular, allowing for the integration and comparison of various analytical components. QIIME has been applied to analyze distal gut bacterial communities from conventionally raised mice, human twins, and germ-free mice colonized with human fecal microbiota. The analysis combined data from multiple studies, including 3.8 million 16S rRNA sequences. QIIME is a robust platform for integrating heterogeneous datasets and providing insights into microbial communities. It is scalable and can be used on various computing platforms, making it suitable for future advancements in sequencing technology. The software is supported by funding agencies and is available at http://qiime.sourceforge.net/. QIIME facilitates the characterization of microbial community patterns in various ecosystems, including human, animal, and environmental systems.QIIME is an open-source software pipeline for analyzing high-throughput microbial community sequencing data. It was developed to address the challenges of handling large datasets generated by high-throughput sequencing technologies, such as pyrosequencing with error-correcting barcodes. QIIME is built using the PyCogent toolkit and supports a wide range of microbial community analyses, including network analysis, diversity histograms, and identification of core microbial communities. It provides graphical displays for data interaction and is highly modular, allowing for the integration and comparison of various analytical components. QIIME has been applied to analyze distal gut bacterial communities from conventionally raised mice, human twins, and germ-free mice colonized with human fecal microbiota. The analysis combined data from multiple studies, including 3.8 million 16S rRNA sequences. QIIME is a robust platform for integrating heterogeneous datasets and providing insights into microbial communities. It is scalable and can be used on various computing platforms, making it suitable for future advancements in sequencing technology. The software is supported by funding agencies and is available at http://qiime.sourceforge.net/. QIIME facilitates the characterization of microbial community patterns in various ecosystems, including human, animal, and environmental systems.