New Gut Microbiome Atlas Brings Researchers Closer to Answering What Makes a Healthy Gut

The human gut microbiome and its link to disease have become of increasing interest to researchers, but a lack of access to high-quality harmonized data has prevented them from determining what exactly constitutes a healthy gut microbiome.

Now, a study published in the journal Genome Research has identified the gut bacteria appearing in individuals with 23 separate diseases across 19 countries. The global study represents the largest of its kind to date.

The findings are presented in a new and open access “Human Gut Microbiome Atlas”. The authors hope the atlas will help researchers and healthcare professionals better understand disease signatures of the gut microbiome and lead to more effective treatments.

Building an accurate profile of global gut health

The human gut microbiome refers to the various bacteria, viruses, fungi and other microbes that inhabit the human gut and help the body perform key functions such as digestion. Recent studies have shown a strong relationship between changes in gut microbiome composition and the development of diseases such as depression, Alzheimer’s and type 2 diabetes.

Despite efforts to expand microbial gene catalogs and an increasing number of metagenome-assembled genomes in the literature, there have been few studies that span across different geographies and diseases. This fragmentation of information has prevented large-scale comparative studies and healthcare professionals from tailoring treatments based on a patient's microbiome.

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In the present study, researchers surveyed 6,014 human gut metagenome samples across North America, Europe and South and East Asia. Using machine models and statistical methods, the researchers classified which bacteria appeared most frequently in healthy individuals and those with specific diseases, linking specific functions to specific bacteria. Of particular note was their finding that Fusobacterium nucleatum and Anaerostipes hadrus had the highest frequencies, enriched and depleted, respectively, across different disease cohorts.

The authors hope that by tagging clusters of microbiome features to specific diseases individual pathways for treating illnesses such as colorectal cancer and Crohn’s Disease may become apparent.

“The discovery of microbiome patterns common across disease will allow researchers to answer what constitutes a healthy or unhealthy gut microbiome,” said Dr. Saeed Shoaie, senior lecturer in systems & synthetic biology at King’s College London and corresponding author. “This will allow healthcare professionals to identify and diagnose diseases with greater clarity and implement effective treatments that target areas of the microbiome, like dietary modifications or even microbiome transplants.”

The authors hope to expand their work to produce oral and skin microbiome atlases to help diagnose and treat illnesses like eczema and psoriasis.  In the future, the researchers hope the atlases could also be used to trace antimicrobial resistance (AMR) in the gut.

The World Health Organization estimates that 1.27 million global deaths in 2019 were directly because of AMR. By tracing which gut bacteria are becoming resistant to antibiotics within global populations, the authors hope to improve and assess the efficacy of efforts to treat disease and combat AMR.

“The threat of AMR requires novel and innovative solutions, and using the microbiome holds great potential for improved diagnosis, surveillance, and treatments. We believe that the human microbiome atlas is an important step to unlocking the power of microbiome for this purpose,” said Dr. Frederick Clasen, research associate at King’s College London and co-author of the study.

The atlas will be updated as new research becomes available to continue to empower healthcare decision-making based on microbiome signatures. The researchers concluded, “This open-access atlas will be updated routinely with the new publicly available gut metagenomics data, including the recently announced One Million Microbiome Project, to provide comprehensive open-access metagenomics data from multiple research centers.”

Reference: Lee S, Portlock T, Chatelier EL, et al. Global compositional and functional states of the human gut microbiome in health and disease. Genome Res. 2024. doi: 10.1101/gr.278637.123

This article is a rework of a press release. Material has been edited for length and content.