GutMeta: online microbiome analysis and interactive visualization with build-in curated human gut microbiome database

Abstract

Background: The human gut microbiome is associated with numerous human diseases. The whole-genome shotgun metagenomics sequencing helps accumulate a massive amount of gut microbiome data. However, few curated integrated platforms are available to explore the vast dataset. Advances in data generation pose new challenges to researchers attempting to analyze, visualize, and reuse published data. Result: GutMeta (human GUT whole-genome shotgun METAgenomics data analysis platform) is a one-stop online human gut metagenomic research platform that integrates a curated database, analyses, and visualizations. First, we built the Human Gut Metagenomics Database (HGMD), which contained taxonomy profiling and metadata of the metagenomics. HGMD collected the published human gut microbiome samples with whole metagenome shotgun (WMGS) sequencing data and consistently performed taxonomy classification using MetaPhlan3 for each sample. The various related metadata information was curated, and phenotypes were according to the MeSH ID. At this moment, HGMD contains 20,898 samples from 91 projects related to 65 diseases. Embedded tools could help users to explore the samples by keywords. Second, GutMeta provides researchers with user-friendly metagenomics analysis modules, including community diversity calculation, differential testing, dimension reduction, disease classifier construction, etc. Then, GutMeta provides corresponding interactive visualizations which can download as Scalable Vector Graphics (SVG), providing high-quality images. Further, GutMeta supplies two additional visualizations for the multi-level taxonomy overview for advanced investigations. GutMeta also supports online editing, including attribute adjustment, recoloring, reordering, and drag-and-drop. Third, GutMeta supports users in building their metagenomics analysis workspaces, including standard profiles uploading and built-in HGMD data import for online customized analyses and visualization. Conclusion: GutMeta offers a solution to improve reproducibility in metagenomic research, with the standardized procedure from input data to downstream analysis and visualization. GutMeta is a free access analysis platform that integrates human gut WMGS sequencing data, nine online bioinformatics analysis and data visualization modules/pipelines, and a customized workspace. GutMeta is avaiable at https://GutMeta.deepomics.org.

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