Integrated Metagenomic and Metabolomic Core

The Integrated Metagenomics and Metabolomics Core (IMMC) will provide a platform that interconnects
Projects 1 and 2. Specifically, IMMC will provide high-quality, metagenomics and targeted metabolomics data,
to be integrated with the probiotics randomized clinical trial and clinical cohort outcomes for Projects 1 and 2,
respectively. The IMMC has already acquired relevant metagenomics and metabolomics data (see Preliminary
data sections E1.2 and F.1.A.2) that supports the experimental rationale and study design for Projects 1 and 2.
To ensure optimal scientific output from the study samples, the IMMC has implemented standardized
procedures for collection of samples from Projects 1 and 2 study sites, and established logistics to coordinate
shipment of samples for analysis, manage inventory, and enable tracking of chain of custody.
For Project 1, IMMC - sub-core 1 will conduct state of the art metagenomics analysis of fecal samples
collected from study participants receiving probiotics supplementation, to profile the changes in the gut
microbial communities. The culture- independent molecular methods will consist of 16S rRNA gene and whole
genome shotgun (WGS) metagenomic sequencing that provide the most comprehensive microbiota profiling.
Rigorous sequence data analysis will utilize a set of advanced computational algorithms, according to taxon-
based or function-based data matrices. IMMC- sub-core 2 will conduct targeted metabolomics analysis of
plasma/serum (Projects 1 and 2) to monitor host and gut-microbiota metabolomes.
The IMMC will collaborate with Projects to develop meaningful study designs, implement effective sample
collection and storage strategies, generate high-quality metagenomics and targeted metabolomics data,
computationally summarize these data and support interpretation of the results. It will implement high-quality
techniques, along with quality control standards, that produce meaningful results in a timely fashion. The IMMC
will also standardize data generation methods across studies to enable integration across Projects and
uncover robust discoveries.
To accomplish these goals the IMMC has established the following aims:
1. Employ metagenomic approaches to generate and analytically summarize project microbiome data.
2. Perform targeted metabolomics analyses to profile plasma/serum metabolites.
3. Manage specimen and data biorepository and facilitate transfer between research Projects.

Grant Number: 5P01AA029542-05
NIH Institute/Center: NIH
Principal Investigator: SHIRISH BARVE