Researchers have launched the NIBN Japan Microbiome Database (NIBN JMD), a large and publicly accessible collection of healthy human gut microbiome data. This new resource contains over 2,000 microbiome samples, each paired with up to 1,000 detailed data points, including demographics, diet, lifestyle, and medical history. It also includes longitudinal data that tracks changes in individuals’ gut microbiomes over time.
The database was created to help scientists better understand how the gut microbiome affects health and disease. Previous microbiome datasets often lacked detailed context or consistency, making it difficult to compare studies or draw broad conclusions. NIBN JMD addresses these problems by using standardized data collection and processing methods, ensuring reliable and comparable results across a diverse range of participants from both urban and rural areas in Japan.
Samples were collected from nine locations across six prefectures, including big cities like Tokyo and Osaka, as well as rural regions like Minamiuonuma. This wide geographic spread improves the database’s regional diversity. The gut microbiome is known to play a critical role in health, influencing conditions such as obesity, infections, inflammation, and cancer. However, past research was limited by incomplete metadata and inconsistent methods.
To build the database, researchers used a custom analysis pipeline called “Snaq” to process 16S rRNA sequencing data, combined with the SILVA database for taxonomy. Shotgun metagenomic sequencing was also performed, with further analysis planned for future releases. The project is led by the National Institutes of Biomedical Innovation, Health, and Nutrition (NIBN), a Japanese organization formed in 2005 through collaboration between the National Institute of Biomedical Innovation and the National Institute of Health and Nutrition.
Currently, NIBN JMD includes 2,273 microbiome samples from 2,068 people. Each sample is linked to extensive metadata, though the level of detail varies by cohort. Age data is grouped to protect participant anonymity. The database runs on a customized MANTA platform, which offers built-in tools for visualizing microbiome data and exploring links to health outcomes. The platform also supports easy integration with other analysis tools and updates automatically as new data becomes available.
While basic data in the database is openly accessible, access to more detailed metadata requires researchers to enter into collaborative agreements and receive ethical approval, ensuring data privacy and responsible use.
NIBN JMD is already helping scientists uncover how gut microbiota relate to diet, bowel habits, and metabolic diseases like obesity and type 2 diabetes. Although the database currently only includes Japanese participants, it marks an important step forward in microbiome research infrastructure. By offering a comprehensive, well-annotated, and user-friendly resource, NIBN JMD aims to accelerate discoveries that could lead to personalized treatments and lifestyle interventions targeting the gut microbiome.
This initiative promises to enhance global efforts to harness the microbiome for better health outcomes in the future.
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