RT Journal
A1 Lee, Sunjae
A1 Portlock, Theo
A1 Le Chatelier, Emmanuelle
A1 Garcia-Guevara, Fernando
A1 Clasen, Frederick
A1 Oñate, Florian Plaza
A1 Pons, Nicolas
A1 Begum, Neelu
A1 Harzandi, Azadeh
A1 Proffitt, Ceri
A1 Rosario, Dorines
A1 Vaga, Stefania
A1 Park, Junseok
A1 von Feilitzen, Kalle
A1 Johansson, Fredric
A1 Zhang, Cheng
A1 Edwards, Lindsey A.
A1 Lombard, Vincent
A1 Gauthier, Franck
A1 Steves, Claire J.
A1 Gomez-Cabrero, David
A1 Henrissat, Bernard
A1 Lee, Doheon
A1 Engstrand, Lars
A1 Shawcross, Debbie L.
A1 Proctor, Gordon
A1 Almeida, Mathieu
A1 Nielsen, Jens
A1 Mardinoglu, Adil
A1 Moyes, David L.
A1 Ehrlich, Stanislav Dusko
A1 Uhlen, Mathias
A1 Shoaie, Saeed
T1 Global compositional and functional states of the human gut microbiome in health and disease
JF Genome Research 
JO Genome Research 
YR 2024 
FD June 01 
VO 34 
IS 6 
SP 967 
OP 978 
DO 10.1101/gr.278637.123 
UL http://genome.cshlp.org/content/34/6/967.abstract 
AB 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.