Microbiome / Gnotobiotic Animal Core

Casey Morrow, Ph.D.
– Co-Director

Casey Weaver, M.D.
– Co-Director

Contact: (205) 934-5705


The overall goal of the new UAB Comprehensive Cancer Center Microbiome/Gnotobiotics Shared Facility (MGSF) is to provide CCC investigators with access to cutting-edge microbiome analysis methodologies and gnotobiotic animal models designed to facilitate and strengthen the quality of CCC-related research.

A pilot CCC Microbiome/Gnotobiotic Shared Facility (MGSF) was started in February 2012 in response to the role that microbial pathogens play in metabolism and energetics that link obesity and cancer, which are major health concerns in the Cancer Center’s catchment area and the entire Southeast. Understanding the role of the microbiome in cancer requires investigation of the interactions among genes of the microbiota and host. Essential to such research is the ability to manipulate and define the microbiota, i.e., develop defined-flora and “humanized” animal models. Gnotobiotic mice transplantation provides a unique advantage to CCC investigators to study disease links and health implications of differences identified from the microbiome analysis (including metagenome analysis).

The following Specific Aims are proposed:

  1. To provide state-of-the-art microbiome analysis services to CCC investigators. The Microbiome component of the MGSF will provide CCC investigators with the full spectrum of resources required to study the microbiota population present in human and animal model research. This includes assistance with experimental design and planning, sample collection and preparation and sequencing of 16S ribosomal genes. In the last year we carried out 5500 microbiome analyses for 87 total users, 46.8% of whom are CCC funded members. We have expanded our services to include metagenomic analysis, and so far have performed metagenome analysis on 28 samples. The Microbiome analysis component works with the CCC Comprehensive Genomics Shared Facility (CGSF) that will provide Next Generation DNA sequencing using the Illumina MiSeq platform at the UAB location.
  1. To provide computational bioinformatics expertise to assist CCC investigators in the analysis and understanding of microbiome data. The Bioinformatics component of the MGSF will provide CCC members with all the necessary resources to fully support the informatics needs required for conducting state-of-the art microbiome and metagenome research. The services are directed at providing: 1) access to information; 2) access to tools; 3) analytical expertise; and 4) research and educational support in the use of the information and tools. The Bioinformatics component will work with the UAB-CCC Biostatistics/ Bioinformatics Shared Facility to provide CCC investigators with the integrated bioinformatics and biostatistics resources required to support their projects, publications, and grant submissions.
  1. To provide gnotobiotic animal services to CCC investigators. The Gnotobiotic Animal component of the MGSF will provide CCC investigators access to gnotobiotic mouse models, assist in developing new gnotobiotic models, assist in “humanizing” these animals by transplantation of archived microbiomes, and support full microbial and immunological analyses of the transplanted microbiota and “humanized” mice. The Gnotobiotic services are now integrated with the Microbiome Analysis and Bioinformatics components to provide guidance to investigators for studies that investigate the interplay of the engrafted microbiomes with the host.
  1. Education and Outreach. Education and outreach is a critical component of the MGSF due to the novel nature of this research, the rapidly evolving understanding of the factors that influence the microbiome, and the manner in which the microbiome can affect the host.


Contact Information:
Casey D. Morrow – Microbiome and Project planning, caseym@uab.edu
Michael Crowley - NextGen sequencing
Elliot Lefkowitz - Bioinformatics
Casey Weaver, Trenton Schoeb and Darrell O’Quinn – Gnotobiotics

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