The goal of this proposal is to build a novel, computational metabolomics platform enabling efficient exploration of bacterial metabolites in the gastrointestinal (GI) tract. It is becoming increasingly evident that microbiota- derived metabolites mediate important signals in the context of inflammation and immunomodulation in the human GI tract. Despite intense interest, only a handful of bioactive microbiota metabolites in the GI tract have been identified. One major challenge is that the spectrum of metabolites present in the GI tract is extremely complex, as the microbiota can carry out a diverse range of biotransformation reactions, including those that are not present in the mammalian host. Classical approaches such as isolating and culturing individual bacteria and identifying metabolites produced in these cultures has not yielded much success, as many bacterial species in the GI tract cannot be cultured under standard laboratory conditions. Moreover, this approach also does not account for community-level interactions between the bacteria nor the interactions between host and bacteria. Thus, alternate methods of discovery are needed. Our approach is to model the microbiota as a metabolic network, and employ a probabilistic search to identify possible biotransformation products of selected metabolites that can be unambiguously attributed to bacteria. A critical new development is to capture the contributions of the host organism through its array of xenobiotic transformation enzymes. Since many of these enzymes exhibit a high degree of substrate flexibility, an algorithm based on pattern matching will be developed to augment the probabilistic search based on reaction definitions. To establish proof-of-concept, we plan to validate the predicted metabolites by performing targeted mass spectrometry measurements on fecal culture samples and characterize the bioactivity of the confirmed metabolites.
Our specific aims are as follows.
In Aim 1, we will build a metabolic network model of GI tract microbiota to enable focused predictions on bacterial biotransformation products. We will analyze the network model by developing a pathway analysis algorithm to predict and rank bacterial metabolites based on the likelihood that the relevant enzymes are expressed in the GI tract microbiota. We will validate the model predictions by analyzing murine fecal cultures as a surrogate experimental system for the GI tract microbiota.
In Aim 2, we will augment the search algorithm of Aim 1 with predictions on probable host modifications computed from pattern recognition analysis of known CYP biotransformations. As in Aim 1, we will perform experimental validation of the model predictions using cultured hepatocytes as a surrogate system for the liver. These studies are expected to demonstrate the significant benefits of computational metabolic pathway analysis for targeted metabolomics, and provide a generally applicable methodology for identifying bioactive microbiota metabolites that are beneficial to human health.

Public Health Relevance

The proposed work seeks to build a computational metabolomics platform for identifying immunomodulatory metabolites derived from the gut microbiota. Successful completion of the proposed work will lay down the foundation for efficient exploration and screening of bioactive metabolites hat are beneficial for human health. Microbiota metabolites with anti-inflammatory properties are naturally occurring metabolites that are already present in the gut, and could represent a safe modality for the treatment of inflammatory diseases of the gut as well as some forms of cancer.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Exploratory/Developmental Grants (R21)
Project #
1R21GM106251-01A1
Application #
8638680
Study Section
Biodata Management and Analysis Study Section (BDMA)
Program Officer
Brazhnik, Paul
Project Start
2014-02-01
Project End
2015-12-31
Budget Start
2014-02-01
Budget End
2014-12-31
Support Year
1
Fiscal Year
2014
Total Cost
$190,981
Indirect Cost
$41,074
Name
Tufts University
Department
Engineering (All Types)
Type
Schools of Engineering
DUNS #
073134835
City
Medford
State
MA
Country
United States
Zip Code
02155
Sridharan, Gautham V; Choi, Kyungoh; Klemashevich, Cory et al. (2014) Prediction and quantification of bioactive microbiota metabolites in the mouse gut. Nat Commun 5:5492