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 |