Global compositional and functional states of the human gut microbiome in health and disease
Journal article, 2024
The human gut microbiota is of increasing interest, with metagenomics a key tool for analyzing bacterial diversity and functionality in health and disease. Despite increasing efforts to expand microbial gene catalogs and an increasing number of metagenome-assembled genomes, there have been few pan-metagenomic association studies and in-depth functional analyses across different geographies and diseases. Here, we explored 6014 human gut metagenome samples across 19 countries and 23 diseases by performing compositional, functional cluster, and integrative analyses. Using interpreted machine learning classification models and statistical methods, we identified Fusobacterium nucleatum and Anaerostipes hadrus with the highest frequencies, enriched and depleted, respectively, across different disease cohorts. Distinct functional distributions were observed in the gut microbiomes of both westernized and nonwesternized populations. These compositional and functional analyses are presented in the open-access Human Gut Microbiome Atlas, allowing for the exploration of the richness, disease, and regional signatures of the gut microbiota across different cohorts.
Author
Sunjae Lee
Gwangju Institute of Science and Technology
King's College London
Theo John Portlock
Royal Institute of Technology (KTH)
Emmanuelle Le Chatelier
University Paris-Saclay
Fernando Garcia-Guevara
Royal Institute of Technology (KTH)
King's College London
Frederick Clasen
King's College London
Florian Plaza Oñate
University Paris-Saclay
Nicolas Pons
University Paris-Saclay
Neelu Begum
King's College London
Azadeh M. Harzandi
King's College London
Ceri Proffitt
King's College London
Dorines Rosario
King's College London
S. Vaga
King's College London
Junseok Park
Korea Advanced Institute of Science and Technology (KAIST)
K. von Feilitzen
Royal Institute of Technology (KTH)
F. Johansson
Royal Institute of Technology (KTH)
C. Zhang
Royal Institute of Technology (KTH)
Lindsey A. Edwards
King's College London
Vincent Lombard
Laboratoire Architecture et Fonction des Macromolécules Biologiques
Aix Marseille University
Franck Gauthier
University Paris-Saclay
Claire J. Steves
King's College London
David Gomez-Cabrero
King's College London
Universidad Publica de Navarra
King Abdullah University of Science and Technology (KAUST)
B. Henrissat
King Abdulaziz University
Technical University of Denmark (DTU)
D. Lee
Korea Advanced Institute of Science and Technology (KAIST)
Lars Engstrand
Karolinska Institutet
Debbie L. Shawcross
King's College London
Gordon Proctor
King's College London
Mathieu Almeida
University Paris-Saclay
Jens B Nielsen
Chalmers, Life Sciences, Systems and Synthetic Biology
2200 Copenhagen N
Adil Mardinoglu
Royal Institute of Technology (KTH)
King's College London
David L. Moyes
King's College London
Stanislav Dusko Ehrlich
University College London (UCL)
University Paris-Saclay
Mathias Uhlen
Royal Institute of Technology (KTH)
Saeed Shoaie
Royal Institute of Technology (KTH)
King's College London
Genome Research
1088-9051 (ISSN) 1549-5469 (eISSN)
Vol. 34 6 967-978Subject Categories (SSIF 2025)
Biological Sciences
DOI
10.1101/gr.278637.123
PubMed
39038849
Related datasets
Human Gut Microbiome Atlas (HGMA) [dataset]
URI: https://www.microbiomeatlas.org/data/bioproj.csv