Our preferred method of shipping microbiome kits from patients’ homes to processing sites uses business reply mail labels. The cost per kit is about $4, and patients can put the collection box directly in their USPS mailbox without arranging a pickup or bringing the sample to a drop-off location. However, BRM-shipping is slow and is NOT TRACKED. These details make it unacceptable for some organizations, such as cooperative groups. Please contact Dan about details for such trails.
Email “AP UNI Customer Service Requests uniprintcustserv@osu.edu” and inquire of a quote for the amount of labels needed with the desired address where samples will be received.
Uniprint will send an estimate of the order and use this as an attachment to the workday Order.
Follow instructions to submit a Uniprint order (https://uniprint.osu.edu/news/2021/02/16/how-request-uniprint-purchase-workday).
Reply to email with Uniprint with the Req number in order to complete the process.
Uniprint will send a proof of the BRM label to approve and printing will begin.
BRM labels will be delivered to your preferred address.
The label will direct the kit to the Kenny Rd receiving center, which will charge the worktags printed on the label. Then, they will direct the kit to the address in the top left of the label (where a return address typically goes).
Welcome! Researching with the Spakowicz lab requires the following training. Please complete the sections relevant to your project using the instructions below. If you have questions about which training is required for your project, please get in touch with Dan. If you have questions about the training logistics, including links on this page, please get in touch with Tiffany Talabere at tiffany.talabere@osumc.edu.
Below is the text we’ve used in protocols for microbiome collection and sequencing.
Gut microbiome
Stool Collection
The study participants will be given a home microbiome collection kit during routine clinical visits. Inside are instructions for collecting stool from their next bowel movement or on a specified day, which is then mailed at room temperature to the processing site or hand delivered at their next clinic visit. (Please see APPENDIX 1 for the instructions included in this box. Written instructions are available in 29 languages, and an online video is available in English.) Briefly, a rigid plastic scaffold or paper sheet with adhesive tabs is placed over the toilet seat to collect stool. A sterile spatula with each kit transfers a small amount of stool to a tube containing nucleic acid stabilizer solution. The tube is then placed in a prepaid mailer and sent directly to the processing site, or the tub is hand-delivered at their next clinic visit. Samples are transferred to cryo-vials and stored at -80C until processed in as few batches as possible to minimize technical variation in the sequencing data.
Stool Processing
Total DNA and RNA will be isolated from stool samples using QIAGEN Power Fecal Pro kits or similar. Total DNA, RNA, or amplicons of bacterial or fungal genes will be sequenced using a depth sufficient to define the community. Microbe or gene abundances will be defined via alignment to reference genomes and de novo assembly.
Additional notes
We often include video instructions to describe the process of affixing the shipping label and shipping by USPS. Contact Dan if you’d like to discuss this further.
For shipping, we also recommend this sample mailing instructions document as an appendix. The processing locations may be:
The purpose of the Center of Microbiome Science is to galvanize and organize the community around the broad types of microbiome science going on around OSU across the different colleges and faculty members and to find some way that we can all work together. It turns out that many of the logistics for actually getting started are specific to your college, and that includes the details of how to collect samples. There’s a lot of overlap with how to generate data from those samples, as well as how to analyze them, but the initial part—the process for collecting samples—is unique to the College of Medicine. Given the number of requests for information that we’ve received, I put together some basic information to get you started.
The main focus is around the logistics. You’re in the College of Medicine. These are my recommendations for how you can collect microbiome samples, where you might generate the data, how to do it internally, if you so desire, and how to analyze it. Then, I want to let you know where to find additional help. I could have said, for all of these things, just talk to us. But the goal is for you to learn how to do this type of research without talking to us at all if you don’t want to.
Examples of How the Microbiome Can Be Used in Practice and Research:
As a Biomarker: There’s been a lot of use of the microbiome as a biomarker for pretty much any disease state that you can think of. There have been groups that have looked at people who have a disease and people who don’t; they look at the microbiome in both populations and ask whether or not there are differences. In one particular area, I find it extremely exciting: in response to immune checkpoint inhibitors (ICIs). Before a person starts treatment, you can take a little bit of their stool. With some error, you can predict whether or not that person is going to be a responder.
As a Therapeutic Target: You can take people who are treatment resistant—they had been on ICIs and became resistant and progressed on them. They were then given a fecal transplant—stool is taken from a person who responded to ICIs and transferred to the person who did not or who had progressed. In some cases, the original person started responding to the same treatment again, just after a fecal transplant; that’s all that was changed.
Amenable to Mechanistic Studies: Stool from patients can be gavaged into preclinical models, which often recapitulate several phenotypes observed in the patient, such as response to ICI treatment. Individual microbes can be gavaged or supplemented into a complex stool gavage to determine the effect of composition changes.
Can Be Useful Additional Aim in a Grant Application: Using the microbiome is another way of adding innovation to a research proposal and of exploring ways to address some of the potential results observed.
What Is the Process?
If you are interested in collecting microbiome samples, how do you do it within the College of Medicine and what are the first steps? Here is a basic workflow that could get you from a grant application to the analysis, without having to talk to any particular person. Of course, you can always reach out to me or the Center of Microbiome Science with questions before you get started.
Step 1: Sample Collection
The kit that’s shown in the picture (right) is a very reasonable way to start. It’s suitable for some, but not all, types of analysis. You can store these in the clinic & they can be handed out or mailed to patients. Typically, once someone has consented to a trial, we give them the kit, which they bring home to collect their sample and mail it directly to the processing center. Each kit costs around $25. (Kits available through the OSUCCC Biospecimen Shared Resource)
Step 2: Sequencing
There are two places we recommend for generating the sequencing data:
The analysis of samples is where an interaction with the Center of Microbiome Science can be especially helpful. AMSL built out a Microbiome Platform to automate regular processing and analyses, with bespoke analysis available as a fee-for-service model. However, the Center of Microbiome Science has established and maintains cutting-edge tools on the Ohio SuperComputing Center clusters, available for access by collaborators or bioinformatics shared resource support staff. In addition, the Center of Microbiome Science supports weekly office hours where project-specific questions can be addressed.
Clinical Protocols
Please see this post for our preferred language and suggested appendices if you want to add microbiome collection to a clinical trial protocol.
Additional information
If you’d like a consultation through CoMS, please use the following link.
Position: Assistant Professor Department: Internal Medicine, Division of Medical Oncology Website: https://u.osu.edu/spakowiczlab/ Email:daniel.spakowicz@osumc.edu Research Keywords: microbiome, cancer, immunotherapy, bioinformatics
Brief summary of research: We study how to use the microbiome as a biomarker of cancer treatment responses and as a therapeutic target to improve treatment outcomes. We support microbiome collection in clinical trials at the OSUCCC and nationally, run our own trials that seek to modify the microbiome through dietary or other interventions, and test for causality using preclinical models. We pride ourselves in offering training in all aspects of the process, from patient interaction and sample processing to sequencing library generation and bioinformatics. We have a variety of computational projects looking for low-abundance microbes in tumors or tissues and inferring their effects.
Anything else you would like to share?: When not sciencing or hanging out with the fam I can be found training for long runs. Hit me up if you’d like to go for a jog and chat about microbes!
