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Table 2 Key information to report within sequenced-based microbiome manuscripts

From: Identifying biases and their potential solutions in human microbiome studies

Processing step Parameters
Sample collection - - Description of samples of interest
- Collection location
- Collection device
- Number of different collection personnel
- Sterile techniques used
- Use of technical replicates
Sample storage - Media used to store samples
- Length of storage and storage conditions
- Length of time spent unpreserved
DNA extraction - DNA extraction method
- If using manufacturer kit:
 ◦ Product name
 ◦ Optional steps used
- Any methods used to reduce or remove possible contaminants
Library preparation - PCR parameters including:
 ◦ Polymerase
 ◦ Cycle number
 ◦ Thermal profile
- Marker gene studies:
 ◦ Primer names and gene target(s)
- Metagenomic shotgun studies:
 ◦ Library preparation kit name/protocol
 ◦ Detailed information about:
  ▪ DNA fragmentation
  ▪ DNA fragment repair
  ▪ Ligation
  ▪ PCR amplification
- Normalization method
- Amount of starting template used
Sequencing - Sequencing platform
- Consumable product names
- Whether demultiplexing or any other sequence pre-processing on-instrument was done
Bioinformatics - All tools used to process raw data along with:
 ◦ Goal of tool
 ◦ Version number
 ◦ Non-default parameters
- Any database names along with their version numbers
- Any statistical tests used to analysis data