Michigan Gastrointestinal Peptide Research Center


Core Facilties


MICROBIOME AND INFLAMMATION CORE

The goal of the Microbiome & Inflammation Core is to provide researchers within the Michigan Gut Peptide Center (UM-MGPRC) access and training for state-of-the-art technologies in culture-independent and culture-based molecular tools to profile the complex community of microbes that exist in and on the human body or animals studied in relevant models of gastrointestinal disease. The different programs that will make up this Core will provide essential services, equipment and education for investigators who are interested in studying interactions between the host and the microbiome. These techniques require significant expertise and many are expensive and/or require sophisticated instrumentation typically unavailable in the laboratories of individual investigators. By offering a centralized source of expertise, instrumentation and resources, the UM-MGPRC gains a number of significant benefits by supporting this shared facility: (i) stable, highly-trained, and experienced personnel to train and oversee analyses, providing consistent performance standards and a high-level of quality control over time, (ii) an improved level of cost-effectiveness achieved by a larger scale of operation, and (iii) access to skilled investigators for consultation on experimental design and interpretation of results. This Core, and its directors, will be adapting to the evolving needs, accumulating knowledge and advancing technology related to the biology of the microbiome and regulation of inflammatory processes.

As currently envisioned, the Microbiome & Inflammation Core will consist of five programs and a bioinformatics interface, led by Dr. Pat Schloss, that also utilizes the resources of The University of Michigan Center for Computational Medicine and Biology (CCMB, http://www.ccmb.med.umich.edu/).

  • Nucleic acid preparation - will facilitate the retrieval of nucleic acid, including genomic DNA and RNA, from human and animal tissue. This nucleic acid will be used for 16S and metagenomic analysis as well as host expression analysis. This program will also provide experimental design assistance to aid investigators in designing protocols that will permit analysis of the microbiome.
  • 16S/metagenome analysis - will facilitate molecular analysis of complex microbial communities. A range of techniques for retrieval of small subunit rRNA-encoding gene sequence information will be available ranging from terminal restriction fragment length polymorphism (T-RFLP) analysis to the construction of 16S clone libraries and 16S variable region pyrosequencing. Assistance with metagenomic sequence analysis using massively-parallel DNA sequencing will also be available.
  • Expression analysis - will facilitate the examination of host responses. Both ELISA-based and RT-PCR-based methods will be available.
  • Microbial cultivation - will provide consultation expertise in traditional and novel methods for bacterial cultivation from host tissues and samples. Novel methods employ cultivation guided by nucleic acid sequence information to allow targeting of specific organisms of interest that are identified by molecular survey techniques, such as those provided by the 16S/metagenome analysis program.
  • Gnotobiotic animal facility - will provide expertise in germ free mouse technology. The ability to re-derive various mouse strains in the germ free state and to selectively colonize with specific microbes will be available in this core facility. Investigators will be able to maintain strains in germ-free or gnotobiotic states and also perform experimental procedures on these animals.
Services
  • Nucleic Acid Isolation
  • Terminal Restriction Fragment Length Polymorphism (T-RFLP) Analysis
  • 16S Clone Libraries
  • 454 Pyrosequencing
  • Expression of inflammatory/regulatory cytokines and genes
  • Microbial Cultivation
  • Germ-free & Gnotobiotic Mouse Facilities
  • Bioinformatics Consultation and Training


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