Overview

As a UCSF 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 analytical platforms.

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 BCMM 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.

We recognize that collaboration is bi-directional. Thus, we offer shadowing opportunities and workshops for investigators to gain hands-on skills in microbiome research. For those with a microbiology background or want to learn on their own, we provide access to supplies, equipment, and protocols required to perform your project.

We are here to assist academic and industry researchers through every step of the project. Services include project planning and management, appropriate sample collection, handling and storage protocols, nucleic acid extraction, quantitative PCR, library preparation, sequencing and data interpretation. As a centralized facility we have developed streamlined workflows and protocols that are optimized for individual sample types.

Our facility is in the Medical Science Building at UCSF. 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.

Pricing

We are a cost-effective resource for basic, clinical and translational science projects. Below is a summary of our approved recharge rates, effective July 1, 2025.

 
Services:Units:Internal 
Rates:		External* NFP Rates:External**
Rates:
DNA Extractioneach$65.69 $82.77 $91.05 
Library Prep (16s RNA / ITS2 Profiling)each$35.90 $45.23 $49.76 
Library Prep (Shotgun Metagenomics)each$99.30 $125.12 $137.63 
Miseq (16S/ITS, 0-300)***per run$839.76 $1,058.10 $1,163.91 
Miseq Micro (30-100)***per run$839.76 $1,058.10 $1,163.91 
Miseq Nano (Fewer than 30)***per run$839.76 $1,058.10 $1,163.91 
Miseq run onlyper run$439.83 $554.18 $609.60 
Nextseq (300-7200)per run$6,950.79 $8,757.99 $9,633.79 
Nextseq (300-7200) excl. laborper run$5,868.36 $7,394.13 $8,133.55 
Nexseq run onlyper run$1,561.65 $1,967.67 $2,164.44 
Dual RNA sample processing (LibPrep and ribodeplete)each$300.06 $378.07 $415.88 
Dual RNA seqeach$3,139.19 $3,955.38 $4,350.92 
WGS Rapid 24each$108.37 $136.55 $150.20 
RNA processing surcharge excl. laboreach$24.34 $30.67 $33.74 
Analysisper hour$147.77 $186.19 $204.81 
Project Managementper hour$147.77 $186.19 $204.81 
Tech Prep (Jr)per hour$76.01 $95.77 $105.34 
Special Consumablespass through at cost  cost + 26%  cost + 38.6% 
DNA and RNA extraction (QIAGEN powerFecal kit)each$68.53 $86.34 $94.98 

* Includes 26% Facilities and Administration Rate

** Includes 10% Surplus Revenue and 26% Facilities and Administration Rate

*** Rates do not include kits, the cost of the kit will be added at cost as special consumables

 

Services: Note: The pricing listed above is our current pricing. However, pricing is adjusted semi-annually and is not guaranteed. For projects that will be processed >3 months from the time of quote generation, we suggest that you add a 10-15% pricing buffer to account for increasing service costs. Actual pricing will be determined at the time the work will be completed by the facility.


 

Consultation and project support

Our team has the expertise to assist with all aspects of microbiome profiling, from study design, sample collection and preservation, sample processing, selection of appropriate sequencing method, generation of quality reads to data analysis. To discuss new or ongoing projects, submit a Request Project Support form on iLab.

Assistance with grant proposals and manuscripts is also available. This includes generation of preliminary data and figures, hypothesis formulation, biological inference, narrative development and dissemination of findings. Most journals follow a strict data release policy and require that the raw data to be deposited in repositories before submitting the manuscript, we can facilitate this process helping investigators meet publication requirements.
 

Sample processing

Samples can be delivered frozen or as extracted nucleic acids. Please send us an email to coordinate sample transfer. We have experience analyzing a range of sample types including intestinal, skin, oral, nasal, blood or vaginal and are happy to work with you to develop protocols for new sample types. Once the study is completed, samples may be collected from the BCMM up to two months following report delivery.
 

Sequencing technologies

16S/ITS amplicon sequencing

This is the most economical, rapid and computationally feasible method for microbiota profiling in both pilot studies and projects involving large volumes of samples. Resultant data will reveal the types and distribution of organisms that make up the microbiota and provide insights on the complexity and structure of these communities. We typically sequence the V4 or V1-V3 regions of the bacterial 16S rRNA gene and ITS2 region for fungi.

cDNA-based 16S/ITS amplicon sequencing

In contrast to traditional DNA-based amplicon sequencing which captures live, dormant and dead microbial cells, we can apply a novel method developed in the Lynch Lab, where RNA is used to produce cDNA from which 16S/ITS amplicons are generated and sequenced. This permits assessment of transcriptionally active members of the microbiota, reducing the signal to noise ratio in associating microbial taxa with phenotypes of interest

Shotgun metagenomics

This approach is useful for examination of the encoded gene capacity of the microbiome, for classification and quantification of specific gene pathways, and identification of specific microbial strains that are differentially enriched or depleted in the populations under study

Whole genome sequencing of pure isolates

Our facility has an Oxford Nanopore MinION device for genome sequencing of microbial isolates. Its long-read capability is useful in characterizing biosynthetic gene clusters, highly repetitive genomic regions and genomic arrangements, and closing sequences of bacterial genomes and plasmids. We are developing a customized workflow for the assembly and annotation of MinION sequencing data, stay tuned!

Dual RNA sequencing

This approach allows for simultaneous detection of host and microbial transcriptomes without the need for predesigned species-specific probes. It is frequently used in resolving macrophage-pathogen crosstalk over the course of infection in in vitro and in vivo models. We are extending the utility of dual RNA seq to microbiome studies for identification of co-expressed host and microbial genes to better understand system-level interactions of microbiomes and their hosts in a range of contexts

 

Data analysis and next steps

In addition to project management and sequencing services, our team can facilitate analyses of microbiome sequence datasets generated for your study. Each analysis package is customized to the project and includes a written report with figures, methods and sequence data files. Analysis is charged based on an hourly rate. Although the actual cost will depend on the total number of samples, the complexity of the study design and analytical approach, most projects can expect to spend $2000+ for analyses.

Sequence-based approaches represent one of many strategies to investigate the composition and function of the microbiome. Based on your results, we can make recommendations for follow-up mechanistic studies and facilitate validation of microbial activities through other BCMM technology hubs such as the Gnotobiotic Mouse Facility, the Quantitative Metabolomics Analysis Center or the Microbial Culture Facility.
 

Meet our team


Rahim Khan, PhD
Manager


TBN
Research Associate


Lu Yang, PhD
Computational Biologist

 

 

 

 

 
 

Ready to get started? Submit a request on iLab.


Frequently asked questions

Why should you collaborate with the Microbial Genomics CoLab?

Specialized in microbiome-based advances: Our team has a keen interest in all things microbial. We want to learn about your project and make the most out of each collaboration by sharing the latest developments in the field and insights from our experiences with studies of similar scale and scope. We offer complimentary half-hour consultation prior to the commencement of each project, please take advantage of this service.

Resourceful network: We work collaboratively to solve problems that are not easily tackled within traditional departments. Our team and extended network are experts in the microbiome field and beyond. Even if we do not have an immediate solution to the problem, we will leverage our network and get your project across the finish line.

Cost-effective pipelines: A centralized microbiome technology hub will increase the efficiency while significantly reducing project costs through bulk extraction and processing of samples.

Standardized approaches: Our team of highly trained specialists will perform all assays using optimized standard operating procedures, ensuring consistency of the data.

How do I get started?

Please plan projects in advance! Turnaround time is queue- and project-dependent and our goal is to have each project result in the highest quality and quantity of data possible. You can fill out our service request form on iLab to initate the process.

How do I acknowledge the Microbial Genomics CoLab?

All work performed in the facility should be acknowledged in presentations, posters, and publications. Acknowledgement is an important benchmark by which we can measure the impact of the facility over time and will be essential for future funding. Please acknowledge us as the "UCSF BCMM Microbial Genomics CoLab Plug-in" when appropriate. If a member of our staff has made intellectual contributions towards the design, method development, analysis or interpretation of your study, we would appreciate consideration of co-authorship. 

What happens if my sequencing run fails?

Pricing for failed reactions will be evaluated on a case-by-case basis. Costs incurred due to a failed extraction conducted by the BCMM will be waived. Library preparation and sequencing failure will be discussed after initial quality control analysis.

What if areas that I need help with are not listed?

Reach out to us anyway! We can come up with a specialized plan or direct you to a third-party service provider.