Table 2 Minimum information about controls and procedures for microbiome studies
From: Guidelines for preventing and reporting contamination in low-biomass microbiome studies
Area | Term | Definition | Possible values |
|---|---|---|---|
Sample collection | Sampling controls | Controls used during the sampling process | Swab or collection vessel left open while sampling; human or PPE swab; swab of equipment/surfaces that may have contacted the sample; preservation material |
Extraction controls | Controls used during nucleic acid extraction | Extraction blanks, extraction and sequencing of individual reagents used, batch number | |
Library prep. controls | Controls used during library preparation for sequencing | Library prep blanks; reagent lot numbers; batch number | |
Laboratory methods | Workspace decontamination | Methods used to decontaminate the workspace where samples were handled | Biosafety cabinet or laminar flow hood; 80% ethanol, bleach, UV-C treatment (time); commercial DNA-degrading solution |
PPE | PPE worn when collecting and handling samples | Gloves (single, double and so on); coveralls, face shields, respirators | |
Positive controls | Positive controls introduced at each step in the workflow | Mock community (cells or DNA); single species spike-in | |
Data processing | Decontamination pipeline | Software tools (including version number) and/or custom scripts used for removal of contaminants from the final dataset | Examples include Decontam, SourceTracker, Squeegee, SCRuB, microDecon and MicrobIEM. Include version number, mode, parameters as relevant. Links to script should be provided as a permanent DOI. |
Contaminant database | Name and release number of any contaminant database used to screen microbiome dataset | ||
Datasets | Control sequences | Raw sequence data from all control samples | Data should be made available either as Supplementary Information linked to the manuscript, or at a permanent DOI address |
Original dataset | Accession numbers for raw microbiome datasets before removal of contaminants | Accession number or permanent DOI | |
Processed dataset | Accession numbers for microbiome datasets after processing and removal of contaminants | Supplementary data included with the manuscript and/or repository accession number |
