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.

1. 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.
2. Uniprint will send an estimate of the order and use this as an attachment to the workday Order.
3. Follow instructions to submit a Uniprint order (https://uniprint.osu.edu/news/2021/02/16/how-request-uniprint-purchase-workday).
4. Reply to email with Uniprint with the Req number in order to complete the process.
5. Uniprint will send a proof of the BRM label to approve and printing will begin.
6. 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).

1. Wetlab training (if applicable)
2. Regular meetings
   1. Gpmtg M 930-11
   2. Project meetings
   1. Carbone Lab meeting Th 10a
   2. CoMS workshops [ bi-weekly, Wed ]
   3. 1:1 (use “Focus Time” if necessary)
3. Computational Training
   1. R/RStudio
      • https://moderndive.com/ 
      • ch1-4 & more if desired
   2. GitHub
      • Create account and send username to DS to be added to the spakowiczlab organization
      • We recommend interacting with git through the application GitHub Desktop.
        • install and authenticate
      • Brief tutorial
   1. OSC
      1. DS will invite you to the relevant project
      2. Tutorials and Training
   2. Library events
      1. Basic and advanced PubMed workshop
      2. Zotero training
4. Identify Key background papers for project
   1. Zotero shared dir
   2. OneDrive
      1. pdfs
      2. PowerPoint presentations from journal clubs
5. Locations of data
   1. OneDrive
   2. GitHub 
   3. T: drive
   4. OSC
6. Setup in lab systems
   1. Google docs
   2. GitHub
   3. Slack
   4. Zotero
   5. ORCid
   6. Outlook Calendar 
   7. OSC
7. Other communication
   1. Introduction @ CLM Fri
      1. Other faculty who regularly attend:: {Carbone, He, Memmott, Kaufman, Dikov, Owen}
      2. Schedule presentation 
   2. Key lab member interactions:
      1. Caitlin Sanders [[ admin ]] 
      2. Other lab members (project-specific)

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.

Training required for everyone

Register for E-protocol

1. Visit the OSU E-protocols website
2. Login using your OSU name.# account
3. Click “Protocol” and follow the instructions

Conflict of Interest Statement

1. Visit the COI Statement website
2. Log in using your OSU name.#
3. Click the “Modify Disclosure” button to update your form.
4. Click the “Submit Disclosure” button on the “Overview and Confirmation” page.

HIPAA and Institutional Data Compliance:

1. Visit the BuckeyeLearn website
2. Search for: HIPAA and Institutional Data Compliance.
3. Select the “Online Class” for the appropriate fiscal year
4. Then click “Launch”.

Responsible Conduct of Research:

1. Visit the CITI training website
2. Select Responsible Conduct of Research [Biomedical]
3. Complete modules with an overall score of 80%.
4. Email the certificate of completion to tiffany.talabere@osumc.edu.

Training for working in the wet lab

Online Risk Assessment Tool

1. Go to the website: Online Risk Assessment Tool http://go.osu.edu/riskassessment
2. Login with your OSU name.#
3. Click the Edit Risk Assessment
   1. Please complete the risk assessment to the best of your knowledge. It will be routed to Dan for review, and he’ll ensure it fits your project.

EHS Online Training:

1. Visit the EHS Online Training website
2. Click on “EHS Online training”
3. Under the program listing dropdown menu
4. Choose Area:
   • Bio-Safety
   • Research Safety
   • Occupational health and safety
5. And Programs:
   • Bloodborne Pathogens Training
   • Biological Safety Training for BSL2 
   • Laboratory Standard Training
   • Radiation Safety Short Course 
   • Building an Emergency Action Plan (BEAP) 
   • Complete the training.
6. Inform tiffany.talabere@osumc.edu upon completion so she can print out your training log for our records.

Training for working with mice:

• Visit the CITI training website
• Select Working With the IACUC
• Complete all modules with a collective score of 80%
• Email the certificate of completion to tiffany.talabere@osumc.edu.

Training to be added to IRB protocols

Human Subjects Protection

1. Visit the CITI training website
2. Select Human Subjects Protection [HSP] (Biomedical) course.
3. Complete modules with a collective score of 80%.
4. Email the certificate of completion to tiffany.talabere@osumc.edu.

Last updated 2023-04-04 by DS

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:
  • Spakowicz Lab
  • 450 Biomedical Research Tower
  • 460 W 12^th Ave
  • Columbus, OH, 43210
    • or
  • BSSR Biorepository
  • 2001 Polaris Parkway Suite 1107
  • Columbus, OH 43240
• Here’s a popular press article about the microbiome. We included this in a welcome folder in some trials to give background on the microbiome.

Check out Dan and Nye on the Emmy Award-winning science show, which aired on December 14, 2022.

UPDATE: 2023-02-06, this position has been filled. Interested candidates should continue to contact Dan to inquire about opportunities.

Click here to view Big10 CRC Lecture.

Click here to view Dan’s Pelotonia interview.