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.

We also provide microbiological research services including anaerobic bacterial isolation and expansion for in vitro and in vivo experiments (culturomics). We also offer expert guidance with respect to microbiome biospecimen collection, clinical microbiome study design, and microbiome preclinical modeling in vitro and in vivo. 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

Resources for Grants

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.

Services

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. Areas of expertise include:

Consultation

Microbiome methods for grant applications and biospecimen collection protocols
Sample collection support, including kits, receiving, aliquoting and storage

Collect & store samples

Biospecimen types supported: stool, oral wash, saliva, skin swabs, tissues, urine, lavages
Dietary monitoring by a research dietician: food frequency questionnaire (FFQ), Nutrition Data System for Research (NDSR) 24-hour recall

Process samples

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