Month: January 2023

Protocol language for microbiome collection

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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 12th 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.