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Guidelines for preventing and reporting contamination in low-biomass microbiome studies
Noah Fierer1, Pok Man Leung2,3, Rachael Lappan2,3
1Department of Ecology and Evolutionary Biology, Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, USA. noah.fierer@colorado.edu.
Nature Microbiology
|June 20, 2025
Summary
This consensus statement provides strategies to minimize contamination in low microbial biomass environments. It offers guidelines for marker gene and metagenomic analyses to ensure reliable microbiome study results.
Area of Science:
- Microbiology
- Environmental Science
- Genomics
Background:
- Low microbial biomass environments, such as human tissues and soils, present unique challenges for DNA sequencing.
- External contamination is a critical concern in low-biomass samples, potentially leading to misleading results.
Purpose of the Study:
- To outline strategies for reducing contamination and cross-contamination in low microbial biomass studies.
- To establish minimal standards for reporting contamination information and removal workflows.
Main Methods:
- Focus on marker gene and metagenomic analyses.
- Recommendations cover all study stages: sample collection, handling, data analysis, and reporting.
Main Results:
- Strategies to mitigate contamination in low microbial biomass environments are detailed.
- Guidelines for identifying and removing contaminants are provided.
Conclusions:
- Researchers must consider contamination at every stage of microbiome studies, especially in low-biomass systems.
- Adoption of these recommendations is urged for accurate and reliable microbiome research.
