The phyloseq R package provides an object-oriented framework for analyzing microbiome census data. It supports importing data from various formats and includes tools for data processing, analysis, and visualization. The package enables reproducible research by allowing users to document, share, and modify analyses. It integrates with other R packages and supports a wide range of statistical and graphical methods, including ordination techniques and distance calculations. The package also facilitates the creation of publication-quality graphics and supports interactive data exploration. Phyloseq is designed to handle phylogenetic sequencing data, including OTU clustering results, and provides functions for analyzing and visualizing microbial community data. It is available on Bioconductor and GitHub, and includes extensive documentation and examples for reproducible research. The package is open-source and freely available, making it a valuable tool for microbiome analysis.The phyloseq R package provides an object-oriented framework for analyzing microbiome census data. It supports importing data from various formats and includes tools for data processing, analysis, and visualization. The package enables reproducible research by allowing users to document, share, and modify analyses. It integrates with other R packages and supports a wide range of statistical and graphical methods, including ordination techniques and distance calculations. The package also facilitates the creation of publication-quality graphics and supports interactive data exploration. Phyloseq is designed to handle phylogenetic sequencing data, including OTU clustering results, and provides functions for analyzing and visualizing microbial community data. It is available on Bioconductor and GitHub, and includes extensive documentation and examples for reproducible research. The package is open-source and freely available, making it a valuable tool for microbiome analysis.