Guidelines for preventing and reporting contamination in low-biomass microbiome studies.
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| Auteurs principaux: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Artículo científico |
| Langue: | en |
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Nature microbiology
2025
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| author | Fierer, Noah Leung, Pok Man Lappan, Rachael Eisenhofer, Raphael Ricci, Francesco Holland, Sophie I Dragone, Nicholas Blackall, Linda L Dong, Xiyang Dorador, Cristina Ferrari, Belinda C Goordial, Jacqueline Holmes, Susan P Inagaki, Fumio Korem, Tal Li, Simone S Makhalanyane, Thulani P Metcalf, Jessica L Nagarajan, Niranjan Orsi, William D Shanahan, Erin R Walker, Alan W Weyrich, Laura S Gilbert, Jack A Willis, Amy D Callahan, Benjamin J Shade, Ashley Parkhill, Julian Banfield, Jillian F Greening, Chris |
| author_facet | Fierer, Noah Leung, Pok Man Lappan, Rachael Eisenhofer, Raphael Ricci, Francesco Holland, Sophie I Dragone, Nicholas Blackall, Linda L Dong, Xiyang Dorador, Cristina Ferrari, Belinda C Goordial, Jacqueline Holmes, Susan P Inagaki, Fumio Korem, Tal Li, Simone S Makhalanyane, Thulani P Metcalf, Jessica L Nagarajan, Niranjan Orsi, William D Shanahan, Erin R Walker, Alan W Weyrich, Laura S Gilbert, Jack A Willis, Amy D Callahan, Benjamin J Shade, Ashley Parkhill, Julian Banfield, Jillian F Greening, Chris Fierer, Noah Leung, Pok Man Lappan, Rachael Eisenhofer, Raphael Ricci, Francesco Holland, Sophie I Dragone, Nicholas Blackall, Linda L Dong, Xiyang Dorador, Cristina Ferrari, Belinda C Goordial, Jacqueline Holmes, Susan P Inagaki, Fumio Korem, Tal Li, Simone S Makhalanyane, Thulani P Metcalf, Jessica L Nagarajan, Niranjan Orsi, William D Shanahan, Erin R Walker, Alan W Weyrich, Laura S Gilbert, Jack A Willis, Amy D Callahan, Benjamin J Shade, Ashley Parkhill, Julian Banfield, Jillian F Greening, Chris |
| collection | PubMed - marine biology |
| contents | Guidelines for preventing and reporting contamination in low-biomass microbiome studies. Fierer, Noah Leung, Pok Man Lappan, Rachael Eisenhofer, Raphael Ricci, Francesco Holland, Sophie I Dragone, Nicholas Blackall, Linda L Dong, Xiyang Dorador, Cristina Ferrari, Belinda C Goordial, Jacqueline Holmes, Susan P Inagaki, Fumio Korem, Tal Li, Simone S Makhalanyane, Thulani P Metcalf, Jessica L Nagarajan, Niranjan Orsi, William D Shanahan, Erin R Walker, Alan W Weyrich, Laura S Gilbert, Jack A Willis, Amy D Callahan, Benjamin J Shade, Ashley Parkhill, Julian Banfield, Jillian F Greening, Chris Humans Biomass DNA Contamination Metagenomics Microbiota Specimen Handling Numerous important environments harbour low levels of microbial biomass, including certain human tissues, the atmosphere, plant seeds, treated drinking water, hyper-arid soils and the deep subsurface, with some environments lacking resident microbes altogether. These low microbial biomass environments pose unique challenges for standard DNA-based sequencing approaches, as the inevitability of contamination from external sources becomes a critical concern when working near the limits of detection. Likewise, lower-biomass samples can be disproportionately impacted by cross-contamination and practices suitable for handling higher-biomass samples may produce misleading results when applied to lower microbial biomass samples. This Consensus Statement outlines strategies to reduce contamination and cross-contamination, focusing on marker gene and metagenomic analyses. We also provide minimal standards for reporting contamination information and removal workflows. Considerations must be made at every study stage, from sample collection and handling through data analysis and reporting to reduce and identify contaminants. We urge researchers to adopt these recommendations when designing, implementing and reporting microbiome studies, especially those conducted in low-biomass systems. |
| format | Artículo científico |
| id | pubmed_40542287 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | Nature microbiology |
| record_format | pubmed |
| spellingShingle | Guidelines for preventing and reporting contamination in low-biomass microbiome studies. Fierer, Noah Leung, Pok Man Lappan, Rachael Eisenhofer, Raphael Ricci, Francesco Holland, Sophie I Dragone, Nicholas Blackall, Linda L Dong, Xiyang Dorador, Cristina Ferrari, Belinda C Goordial, Jacqueline Holmes, Susan P Inagaki, Fumio Korem, Tal Li, Simone S Makhalanyane, Thulani P Metcalf, Jessica L Nagarajan, Niranjan Orsi, William D Shanahan, Erin R Walker, Alan W Weyrich, Laura S Gilbert, Jack A Willis, Amy D Callahan, Benjamin J Shade, Ashley Parkhill, Julian Banfield, Jillian F Greening, Chris Humans Biomass DNA Contamination Metagenomics Microbiota Specimen Handling Guidelines for preventing and reporting contamination in low-biomass microbiome studies. Fierer, Noah Leung, Pok Man Lappan, Rachael Eisenhofer, Raphael Ricci, Francesco Holland, Sophie I Dragone, Nicholas Blackall, Linda L Dong, Xiyang Dorador, Cristina Ferrari, Belinda C Goordial, Jacqueline Holmes, Susan P Inagaki, Fumio Korem, Tal Li, Simone S Makhalanyane, Thulani P Metcalf, Jessica L Nagarajan, Niranjan Orsi, William D Shanahan, Erin R Walker, Alan W Weyrich, Laura S Gilbert, Jack A Willis, Amy D Callahan, Benjamin J Shade, Ashley Parkhill, Julian Banfield, Jillian F Greening, Chris Humans Biomass DNA Contamination Metagenomics Microbiota Specimen Handling Numerous important environments harbour low levels of microbial biomass, including certain human tissues, the atmosphere, plant seeds, treated drinking water, hyper-arid soils and the deep subsurface, with some environments lacking resident microbes altogether. These low microbial biomass environments pose unique challenges for standard DNA-based sequencing approaches, as the inevitability of contamination from external sources becomes a critical concern when working near the limits of detection. Likewise, lower-biomass samples can be disproportionately impacted by cross-contamination and practices suitable for handling higher-biomass samples may produce misleading results when applied to lower microbial biomass samples. This Consensus Statement outlines strategies to reduce contamination and cross-contamination, focusing on marker gene and metagenomic analyses. We also provide minimal standards for reporting contamination information and removal workflows. Considerations must be made at every study stage, from sample collection and handling through data analysis and reporting to reduce and identify contaminants. We urge researchers to adopt these recommendations when designing, implementing and reporting microbiome studies, especially those conducted in low-biomass systems. |
| title | Guidelines for preventing and reporting contamination in low-biomass microbiome studies. |
| topic | Humans Biomass DNA Contamination Metagenomics Microbiota Specimen Handling |
| url | https://pubmed.ncbi.nlm.nih.gov/40542287/ |