Microbial Genomics Core

Overview of Services

As a collaborative laboratory (CoLab) plug-in, our mission is to foster connections among interdisciplinary researchers who share a common interest in discovering the biomedical potential of the microbiome. The Microbial Genomics CoLab Plug-in represents a new model for research and training at UCSF, offering collaborative data generation and analytical support for intramural and extramural investigators in parallel with embedded, experiential training opportunities in sequence-based microbiome profiling.

By providing collaborative expertise in next-generation sequencing, we facilitate the exploration of microbiome membership, gene content and transcriptional activity in relation to host outcomes and environmental exposures. We believe this approach in conjunction with complementary tools available within the Benoiff Center for Microbiome Medicine will lead to identification of actionable microbial targets and add a powerful new dimension to the diagnosis and treatment of medical conditions with unmet needs.

Our team has the expertise to offer assistance in the following areas:
- Project planning and management
- Sample collection, handling and storage recommendations
- Nucleic acid extraction
- Quantitative PCR
- Library preparation and sequencing
- Data interpretation
- Dissemination of findings

As a centralized facility, we are a cost-effective resource for basic, clinical and translational studies. We have developed streamlined workflows and optimized protocols for individual sample types. Our technology hub is located in the Medical Science Building. Infrastructure for microbiome analyses includes dedicated pre- and post-PCR spaces, Illumina NextSeq and MiSeq instruments, Oxford Nanopore MinION and access to HiSeq and NovaSeq platforms and HPC cluster.

We recognize that collaboration is bi-directional. Shadowing opportunities and workshops are available to investigators upon request. 

Leadership (Interim)

Name Title Phone Email 
Rahim Khan, PhD Manager   rahim.khan@ucsf.edu

Location and hours of operation

Hours Location
Monday-Friday 10am-5pm
513 Parnassus Avenue, S363

Links and Resources

  1. Microbial Genomics Core


Name Role Phone Email Location
Rahim Khan



Service list

Search available services: View: by category alphabetically
Project and Method Development (3)
Sample Processing (3)
Bacterial 16S rRNA Sequencing (2)
Fungal ITS sequencing (1)
Shotgun Metagenomics (2)
Analysis (1)
Sequencing (9)