GutBiomeDB: an integrated human gut microbiome database of 168 464 samples
Related Experiment Video
Updated: Nov 6, 2026

Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging
Published on: July 9, 2021
Jinxia Zhai1, Bao-Hai Liu2, Lian-Yi Guo2
1Department of Gastroenterology, First Hospital of China Medical University, Shenyang 110001, Liaoning Province,China.
Abstract:
The gut microbiome plays an important role in maintaining human health. Despite the rapid growth of literature and publicly accessible data on the gut microbiome, a large-scale, well-curated database integrating a unified matrix with multiple analytical tools is still lacking. Here, we introduced GutBiomeDB, a comprehensive database and analysis platform for the human gut microbiome. GutBiomeDB contains 168 464 samples from 482 BioProjects, spanning 72 countries, 224 disease conditions, and seven life stages. To improve the reusability and accessibility of data, the uniformly processed taxonomic profiles generated by Abdill et al. were reused without reprocessing to construct a matrix of 4680 taxa and 3142 genera, and disease, life-stage, sex, and geographic metadata were manually curated by our team. Additionally, GutBiomeDB offers four tools for in-depth analysis: "Differential Analysis" for comparing diversity and abundance of user-selected cohorts and performing random-effects meta-analysis across projects; "Interaction Network" for comparing disease and healthy-control co-occurrence networks; "Lifecycle Atlas" for visualizing genus trajectories across seven life stages; and "Health Index" for searching similar samples and scoring uploaded genus profiles. GutBiomeDB serves as a versatile and valuable resource for advancing a broad spectrum of gut microbiome research and clinical relevance. GutBiomeDB is freely accessed at https://gutbiomedb.online.
Related Concept Videos
Introduction to the Human Microbiota
Microbiota of the Large Intestine
Overview of Human Digestion
Microbiota of the Stomach and Small Intestine
Microbiota of the Urogenital Tract
Functions of the Gut Microbiota
