TY  - JOUR
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
Y1  - 2024/06/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 967 
EP  - 978 
DO  - 10.1101/gr.278637.123 
VL  - 34 
IS  - 6 
UR  - http://genome.cshlp.org/content/34/6/967.abstract 
N2  - 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. 
ER  -