Table 1 List of MICROCOSM Consensus Agreement protocols available
From: Standardization of microbiome studies for urolithiasis: an international consensus agreement
Protocol | Description | Location of full information in Supplementary information or server |
|---|---|---|
Instructions for MWAS | Details the objectives of the consensus, the protocols available and how to use the server/automated analytical pipeline | Supplementary data pages 1–6 |
Metadata collection | ||
Metadata definitions for 16S and shotgun studies | Details the specific terms and definitions to use for clinical data to be consistent across studies | Supplementary data pages 7–10 Table S1 |
MICROCOSM questionnaire for patients | A sample questionnaire that can be modified and included as part of an IRB application at the investigator’s home institution | Supplementary data pages 30–50 |
Sample collection | ||
Mid-stream voided urine sample collection protocol for patients | A protocol that details how patients can self-collect urine samples and ship them to a receiving institution | Supplementary data pages 11–14 |
Urine collection at time of procedure for physicians | A protocol that details the collection of upper urinary tract urine by physicians | Supplementary data pages 15–16 |
Urine sample collection form | A sample urine collection form to track urine specimens | Supplementary data page 17 |
Stool collection protocol for patients | A protocol that details how patients can self-collect stool samples and ship them to a receiving institution | Supplementary data pages 18–21 |
Stool sample collection form | A sample stool collection form to track urine specimens | Supplementary data page 22 |
Stone sample collection and processing for physicians | A protocol that details the collection and processing of kidney stone samples by physicians/investigators | Supplementary data pages 23–24 |
Sample processing | ||
Urine processing for investigators | A protocol that details storage, DNA extraction and sequencing of urine samples | Supplementary data pages 25–26 |
Stool processing for investigators | A protocol that details storage, DNA extraction and sequencing of stool samples | Supplementary data pages 27–29 |
Data analysis | ||
16S mapping file template | Template files with standardized variables for clinical data. The mapping file will be populated with data collected from patients | On server |
Shotgun metadata template | On server | |
