New Japanese database reveals how gut microbes and diet connect

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With the launch of the NIBN Japan Microbiome Database, scientists gain an unprecedented window into how lifestyle and diet shape our microbiome and influence long-term health.

Research: NIBN Japan Microbiome Database, a database for exploring the correlations between human microbiome and health. ​​​​​​​Image Credit: Shutterstock

In a recent study published in Scientific Reports, researchers introduced the NIBN Japan Microbiome Database (NIBN JMD), an extensive, publicly available database of diverse, healthy human microbiome profiles (comprising more than 2,000 microbiome samples) annotated with up to 1,000 metadata points per sample, as well as longitudinal study outcomes.

The database aims to facilitate and progress future microbiome association studies and medical research by providing researchers with an exhaustive baseline dataset against which gut microbiome impacts and causal associations can be compared, paving the way for microbiome-associated chronic disease and lifestyle interventions. This article describes the NIBN JMD database, its features, and potential applications.

Background

A growing body of research underscores the importance of the human gut microbiome in shaping host health and disease. Studies have established a strong bidirectional association between gut microbiome features (the composition and relative densities of gut flora) and clinical outcomes, including obesity, infections, inflammation, and even cancers.

While substantial advances in next-generation sequencing technologies (including genomics, proteomics, and transcriptomics) have provided scientists with unprecedented amounts of microbiome data, existing datasets suffer from the common demerits of inadequate metadata and contextual annotation. Furthermore, conventional databases provide summary statistics computed by aggregating data from multiple studies, but they fail to account for inter-study methodological differences.

These demerits severely hinder generalizable, large-scale investigations of microbiome-health interactions, thereby preventing the discovery and deployment of interventions against a broad spectrum of diets, lifestyles, and diseases. This necessitates the development of a standardized human microbiome database comprising both diverse sequencing data and thorough metadata annotation, which would facilitate leveraging the gut microbiome’s full potential in mitigating human disease and promoting global well-being.

What is NIBN JMD?

The National Institutes of Biomedical Innovation, Health, and Nutrition (NIBN, formerly NIBIOHN) is a Japanese collaborative research effort between the National Institute of Biomedical Innovation (NIBIO) and the National Institute of Health and Nutrition (NIHN). Established in 2005, the organization aims to advance biomedical innovation, nutrition, and pharmaceutical output of the Japanese population.

NIBN recognized gaps in current human microbiome databases and addressed this by collating fecal samples and extensive metadata from both its own extensive research network and multiple collaborators to generate one of the largest human microbiome datasets in existence. Named the ‘NIBN Japan Microbiome Database (NIBN JMD)’, this novel database, which is publicly accessible with some restrictions, aims to unleash the human gut microbiome’s true clinical potential through unprecedented metadata annotation and a self-updating design.

The database currently comprises 2,273 microbiome samples from 2,068 subjects, each of which is linked to up to 1,000 metadata points, encompassing participant demographics, diets, lifestyles, physical activity levels, and medical histories. While all samples have basic metadata, the level of detail depends on the specific cohort. The database also includes collaborator-derived longitudinal samples, enabling analyses of temporal microbiome dynamics. Notably, all data processing adhered to standardized protocols to maintain consistency and reliability across a diverse array of samples.

How was NIBN JMD developed, and what are its key features?

Researchers utilized a Snakemake pipeline for QIIME2, called ‘Snaq’, to process 16S rRNA sequencing data, while separate in-house pipelines were employed for shotgun metagenomic data. The latter pipelines include provisions for automation of NCBI-compliant taxonomic assignment (Kraken 2, Bracken, and MetaPhlAn), functional profiling (FMAP), and metadata annotation. The paper notes that while shotgun sequencing has been performed, the full analysis results will be available in a future version of the database.

NIBN JMD was built on a custom implementation of the MANTA platform, providing researchers with a spectrum of in-built multifactorial analysis tools capable of visualizing microbiome-health associations and exploring correlations within the data. Researchers also developed an in-house script to automate the importing and processing of data from new and future samples.

Most importantly, NIBN JMD represents a rich, well-structured dataset that is architecturally focused on user-friendly access and capable of integration with most gold-standard analytical tools. Its public-facing interface supports open science and hopes to revolutionize future collaborative microbiome studies. While basic data is openly available, access to more extensive metadata requires a collaborative agreement and Institutional Review Board (IRB) approval, ensuring the ethical handling of data.

Conclusions

NIBN JMD represents a significant advancement in microbiome research infrastructure, providing scientists with a richly annotated, publicly accessible resource —one of the largest and most comprehensive of its kind. It complements other global resources with its high consistency and interactive analysis tools. This database has the potential to accelerate discoveries in microbiome science, inform personalized health strategies, and expedite the development of interventions that leverage the microbiome.

It has already been applied in studies that have established associations between gut microbiota and factors such as dietary patterns (including barley and vitamin B1 intake), bowel habits, and metabolic conditions like obesity and type 2 diabetes. While its current restriction to only Japanese participants restricts its global generalizability, it presents the first step towards a healthier tomorrow.