NIBN JMD

New healthy society with the gut microbiome database

We are developing basis for drug development for various diseases including pre-symptomatic state, functional foods,
and healthcare products by elucidating the biological regulatory mechanism mediated by the intestinal environment formed from the gut microbiota and nutrients or dietary components.
Furthermore, along with supporting the accelerated development of related fields, we will contribute to the realization of a healthy and long-lived society.

Others

2026.02.05

Changes to NIBN JMD data access policy.

To ensure continuous database updates and improve our services, starting February 5th, 2026, users must log in to access NIBN JMD data. Please submit the application form for creating NIBN JMD account. (Application Form ⇒ [Download])

Accounts are valid for one year. If you wish to continue using the service, please register again.
Publication

2025.07.28

The following paper has been published.
- Hosomi K, Maruyama S, Matsuoka T, Furuta M, Tojima Y, Uchiyama K, Morita M, Kawashima H, Kobayashi T, Kunisawa J (2025) Metabolite-mediated interactions and direct contact between Fusobacterium varium and Faecalibacterium prausnitzii. Microbiome 13(1):175. PMID: 40721806. doi: 10.1186/s40168-025-02168-w.
Publication

2025.06.04

The following paper has been published.
- Chen YA, Kawashima H, Park J, Mohsen A, Hosomi K, Nakagata T, Murakami H, Nanri H, Miyachi M, Kunisawa J, Mizuguchi K (2025) NIBN Japan Microbiome Database, a database for exploring the correlations between human microbiome and health. Sci Rep 15(1):19640. PMID: 40467839. doi: 10.1038/s41598-025-04339-z.

Outline

Recent research has revealed that gut bacteria have a greater impact on our health than previously thought, such as obesity, inflammation, infections and cancer. We have embarked on research to build an gut microbiome database for healthy people since 2015 and recently developed NIBN JMD (Japan Microbiome Database), one of the world's largest gut microbiome database, being public for some data.
In addition to gut microbiota data obtained by 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing, NIBN JMD stores various data related to lifestyle such as diet, nutritional intake, and physical activity (phenotypic metadata). We collected annual data as well as oral and skin microbiome data for some participants. Furthermore, analysis using MANTA, an integrated analysis platform we developed, which enables association analysis and visualization, is also possible.
The data of NIBN JMD is expected to be used in various researches, such as understanding the characteristics of the gut microbiome of Japanese people or elucidating the relationship between health and disease conditions and gut microbiome.

Gut microbiome

Food intake

Physical activity

Features

Characteristics of the NIBN JMD

An integrated microbiome database that includes abundant metadata such as lifestyle habits and biological factors, etc., in cooperation with local governments, companies, and research institutes in Japan

Large cohort database

One of the largest gut microbiome database in the world with abundant related data
Highly reliable

A high-quality database built by conducting from sampling to data processing in-house under strict conditions
Integrated analysis platform

In addition to the database functions, association analysis and visualization are possible