@article{Lee01062024,
author = {Lee, Sunjae and Portlock, Theo and Le Chatelier, Emmanuelle and Garcia-Guevara, Fernando and Clasen, Frederick and Oñate, Florian Plaza and Pons, Nicolas and Begum, Neelu and Harzandi, Azadeh and Proffitt, Ceri and Rosario, Dorines and Vaga, Stefania and Park, Junseok and von Feilitzen, Kalle and Johansson, Fredric and Zhang, Cheng and Edwards, Lindsey A. and Lombard, Vincent and Gauthier, Franck and Steves, Claire J. and Gomez-Cabrero, David and Henrissat, Bernard and Lee, Doheon and Engstrand, Lars and Shawcross, Debbie L. and Proctor, Gordon and Almeida, Mathieu and Nielsen, Jens and Mardinoglu, Adil and Moyes, David L. and Ehrlich, Stanislav Dusko and Uhlen, Mathias and Shoaie, Saeed}, 
title = {Global compositional and functional states of the human gut microbiome in health and disease},
volume = {34}, 
number = {6}, 
pages = {967-978}, 
year = {2024}, 
doi = {10.1101/gr.278637.123}, 
abstract ={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.}, 
URL = {http://genome.cshlp.org/content/34/6/967.abstract}, 
eprint = {http://genome.cshlp.org/content/34/6/967.full.pdf+html}, 
journal = {Genome Research} 
}