Microbiome Core
The Microbiome Shared Resource (MB-SR) is a leading-edge, multidisciplinary service center dedicated to helping researchers at City of Hope expand our understanding of microbiome dynamics using high-efficiency, best-in-class standards and state-of-the-art science.
The MB-SR infrastructure supports a wide array of assays to characterize the microbiome, including services from genomic and metabolomic analyses to multi-omics bioinformatics and data science support.
In addition to our core services, we provide microbiological research support including anaerobic bacterial isolation and expansion for in vitro and in vivo experiments (culturomics). Our team also offers expert guidance with respect to microbiome biospecimen collection, clinical microbiome study design, and microbiome preclinical modeling in vitro and in vivo. Looking ahead, our goals include enabling future interventional studies incorporating microbiome profiling of trial participants, as well as studies of therapeutic strategies targeting the microbiome, ranging from fecal microbiota transplantation, bacterial cell therapies produced under good manufacturing processes (GMPs) and microbiome-modulating molecular inhibitors.
Using the Facility
To convey MB-SR collaborative expertise in support of grant applications, we can provide a biosketch and letter of support tailored to the planned application. The following generic statement is provided as a resource:
MB-SR provides a comprehensive bioinformatics research pipeline for microbiome studies and supports preclinical and interventional studies of microbiome therapeutics. Its services are available to all City of Hope researchers.
The MB-SR performs standard and customized microbiome analyses and uses state-of-the-art sequencing technologies and bioinformatics tools. It provides expertise and consulting in study design, sample collection handling and analysis. MB-SR partners with other Shared Resources to provide these services.
Areas of expertise include:
Consultation
- Microbiome methods for grant applications and biospecimen collection protocols
- Sample collection support, including kits, receiving, aliquoting and storage
Process samples
- Biospecimen types supported: stool, oral wash, saliva, skin swabs, tissues, urine, lavages
- Dietary data collection led by a research dietitian: food records, 24-hour recalls, and food frequency questionnaires
- Extraction: DNA, RNA
- Sequencing: 16S (V4), short read shotgun DNA sequencing, short read shotgun RNA sequencing
- Microbiome-related metabolomics offered by Integrated Mass Spectrometry Shared Resource (IMS-SR): short-chain fatty acids, bile acids, indoles
- Culturomics (microbiological cultivation)
Analysis
- Bioinformatics analysis
- Statistical support
- Publication-ready visualizations
- Post-analysis consultation on data interpretation and future studies
Current pricing can be found on iLab Solutions.
Leadership
Robert R. Jenq, M.D., is a Professor & Director of the City of Hope Microbiome Program, Department of Hematology and Hematopoietic Cell Transplantation.
Jennifer Karmouch, Ph.D., is the Director of the Microbiome Core and Co-Director of the Microbiome Program at City of Hope.
