MicrobiomePhylo: A New Tool for Metabarcoding Data Downstream Analysis - A Real-World Data Analysis Demonstration

Abstract

The field of microbiome research has rapidly expanded, driven by advancements in sequencing technologies that generate vast amounts of data. To navigate this complexity, MicrobiomePhylo has been developed as a web platform tailored for the downstream analysis of microbiome amplicon sequencing data. It stands out for its ability to process QIIME2 artifact files (.qza), offering an intuitive interface, extensive analytical functions, and advanced visualization features, making it indispensable for bioinformaticians and biologists alike. MicrobiomePhylo enhances the understanding of complex datasets by facilitating detailed analysis and visualization. Its effectiveness is showcased through the analysis of the "Moving Pictures" tutorial dataset from QIIME2, a benchmark in microbiome research, featuring 16S rRNA gene sequencing data from various sample types over time. The platform supports a comprehensive workflow including data upload, pre-processing, refinement, visualization, exploration, and advanced statistical analysis. Features include data filtering, rarefaction, and diverse visualizations like barplots, boxplots, and heatmaps. Advanced analyses cover alpha and beta diversity, abundance analysis, differential abundance analysis, and correlation studies, backed by robust statistical methods. A demonstration with the "Moving Pictures" dataset highlights MicrobiomePhylos capability to manage real-world data. Customization options for variables, taxonomic levels, plot dimensions, and group highlighting improve result interpretability and visual appeal. Analysis at the phylum level across different body sites reveals insights into microbial composition and diversity. The generated visualizations distinguish microbial community compositions and taxa abundance between body sites, emphasizing the site-specific nature of the human microbiome. ImportanceThe significance of MicrobiomePhylo in microbiome research is profound. As sequencing technologies advance, generating vast datasets, researchers face the challenge of analyzing this data efficiently. MicrobiomePhylo, a web platform designed for microbiome amplicon sequencing data analysis, directly processes QIIME2 artifact files (.qza), offering an accessible interface for both bioinformaticians and biologists. Its comprehensive analytical and advanced visualization capabilities are crucial for understanding complex datasets, enabling deeper insights into microbial composition and diversity. The platform supports a full workflow from data upload to advanced statistical analysis, including data filtering, rarefaction, and various visualizations for taxa abundances, correlations with continuous variables, diversity and more. This facilitates a thorough investigation of microbiome data, making MicrobiomePhylo an indispensable tool in the field, enhancing our understanding of the microbiome through specialized, user-friendly analysis capabilities.