Summary of project PR000804

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR000804. The data can be accessed directly via it's Project DOI: 10.21228/M8RM32 This work is supported by NIH grant, U2C- DK119886.


Project ID: PR000804
Project DOI:doi: 10.21228/M8RM32
Project Title:A large library of gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome studies
Project Type:Metabolite profiling of human stool from a healthy cohort
Project Summary:Here, we present the Broad Institute-OpenBiome Microbiome Library (BIO-ML), a comprehensive collection of 7,758 gut bacterial isolates with 3,632 paired genome sequences, and densely sampled multi-omic time series from many individual humans. Our longitudinal data reveal (1) that microbial species maintain stable population sizes within and across humans, (2) that commonly used ‘omic survey methods are more reliable when using averages over multiple days of sampling, (3) that variation of gut metabolites within people over time is driven by amino acid levels, while differences across people are driven by differences in bile acids, and (4) that functional evolution and genomic diversification can be used to infer eco-evolutionary dynamics and in vivo selection pressures for strains within individual people. The BIO-ML is a unique resource that will enable hypothesis-driven microbiome research and the rational design of microbial therapeutics.
Institute:Broad Institute of MIT and Harvard
Department:Metabolomics Platform
Last Name:Avila-Pacheco
First Name:Julian
Address:415 Main Street, Rm 7175, Cambridge, MA, 02142, USA
Contributors:Mathilde Poyet, Mathieu Groussin, Sean M Gibbons, Julian Avila-Pacheco, Xiaogang Jiang, Sean M Kearney, Allison R Perrotta, Shijie Zhao, Tammi Lieberman, P K Swanson, Mark Smith, Shane Roesemann, Jessica E Alexander, Scott A. Rich, Jonathan Livny, Hera Vlamakis, Clary Clish, Kevin Bullock, Amy Deik, Justin Scott, Kerry Pierce, Ramnik Xavier, Eric J Alm

Summary of all studies in project PR000804

Study IDStudy TitleSpeciesInstituteAnalysis
(* : Contains Untargted data)
(* : Contains raw data)
ST001192 A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research Homo sapiens Broad Institute of MIT and Harvard MS* 2019-07-17 1 180 Uploaded data (42M)*