Summary of project PR001706

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 PR001706. The data can be accessed directly via it's Project DOI: 10.21228/M8642W This work is supported by NIH grant, U2C- DK119886.


Project ID: PR001706
Project DOI:doi: 10.21228/M8642W
Project Title:Integration of Meta-Multi-Omics Data Using Probabilistic Graphs and External Knowledge
Project Summary:Multi-omics has the promise to provide a detailed molecular picture for biological systems. Although obtaining multi-omics data is relatively easy, methods that analyze such data have been lagging. In this paper, we present an algorithm that uses probabilistic graph representations and external knowledge to perform optimum structure learning and deduce a multifarious interaction network for multi-omics data from a bacterial community. Kefir grain, a microbial community that ferments milk and creates kefir, represents a self-renewing, stable, natural microbial community. Kefir has been shown to associate with a wide range of health benefits. We obtained a controlled bacterial community using the two most abundant and well-studied species in kefir grains: Lentilactobacillus kefiri and Lactobacillus kefiranofaciens. We applied growth temperatures of 30°C and 37°C, and obtained transcriptomic, metabolomic, and proteomic data for the same 20 samples (10 samples per temperature). We obtained a multi-omics interaction network, which generated insights that would not have been possible with single-omics analysis. We identified interactions among transcripts, proteins, and metabolites suggesting active toxin/antitoxin systems. We also observed multifarious interactions that involved the shikimate pathway. These observations helped explain bacterial adaptation to different stress conditions, co-aggregation, and increased activation of L. kefiranofaciens at 37°C.
Institute:University of Nebraska -Lincoln
Last Name:Alvarez
First Name:Sophie
Address:1901 Vine st, Lincoln, Nebraska, 68588, USA

Summary of all studies in project PR001706

Study IDStudy TitleSpeciesInstituteAnalysis
(* : Contains Untargted data)
(* : Contains raw data)
ST002741 Integration of Meta-Multi-Omics Data Using Probabilistic Graphs and External Knowledge Lentilactobacillus kefiri University of Nebraska-Lincoln MS 2023-08-10 1 20 Uploaded data (810.1M)*