Meta-analysis of 22,710 human microbiome metagenomes defines an oral-to-gut microbial enrichment score and associations with host health and disease
Abstract
Abstract Large public datasets of the human microbiome now exist but combining them for large-scale analysis is difficult due to a lack of standardization. We developed curatedMetagenomicData (cMD) 3, a uniformly processed collection of over 22,000 human microbiome samples with manually curated metadata from 94 studies and 42 countries. This large and diverse resource allows for meta-analysis of the links between microbes and human health. Through meta-analysis, we identified hundreds of microbial species and thousands of microbial functions significantly associated with a person’s sex, age, body mass index, and disease status, and catalog these as references. We developed an “oral enrichment score” (OES) based on the relative abundance of bacteria typically found in the oral cavity and not in the gut. Higher OES in the gut is a consistent feature in individuals with disease, suggesting that the relative abundance of oral bacteria in the gut is a simple and quantifiable signal of altered microbiome health. These analyses identify modest but widely shared patterns in human microbiomes, serving as a reproducible and readily updatable reference.
Article Details
Authors (37)
Paolo Manghi
Giacomo Antonello
Lucas Schiffer
Davide Golzato
Andres Wokaty
Francesco Beghini
Chloe Mirzayi
Kaelyn Long
Kai Gravel-Pucillo
Gianmarco Piccinno
Samuel David Gamboa-Tuz
Arianna Bonetti
Giacomo D’Amato
Rimsha Azhar
Kelly Eckenrode
Fatima Zohra
Valentina Giunchiglia
Marisa Keller
Anna Pedrotti
Ilya Likhotkin
Shaimaa Elsafoury
Ludwig Geistlinger
Aitor Blanco-Miguez
Andrew Maltez Thomas
Moreno Zolfo
Marcel Ramos
Mireia Valles-Colomer
Sabrina Tamburini
Francesco Asnicar
Heidi E. Jones
Curtis Huttenhower
Broad Institute of MIT and Harvard
Vincent Carey
Brigham andWomen’s Hospital, Boston, MA, USA.
Sean Davis
Edoardo Pasolli
Sehyun Oh
Nicola Segata
Levi Waldron