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Scrubbing contaminated microbiomes

Nature Reviews Microbiology volume 21, page 554 (2023)Cite this article

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This Genome Watch highlights new computational approaches aimed at circumventing contamination in low-biomass microbiome studies.

Contamination, the elephant in the room in microbiome research, frequently arises due to inadequate or improper use of controls in microbiome experiments. When neglected, it can create substantial hurdles when analysing count-based microbiome data and can often confound or mask the interpretation of true biological signals. This issue becomes particularly pertinent for microbiome studies using human tissues that are presumed to have no or very low microbial biomass, making them highly susceptible to contaminants introduced during the sampling or laboratory processes. Despite the routine use of experimental controls, complete elimination of contaminants is still one of the most challenging tasks in microbiome research. Recent claims regarding the existence of placental1 and blood2 microbiomes have been met with considerable scepticism, with many attributing these findings to contaminations. This underscores the need for computational methods that can efficiently remove contaminants (decontamination) to minimize their impact on biological interpretations.

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  1. Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK

    Yan Shao

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  1. Yan Shao
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Correspondence to Yan Shao.

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Shao, Y. Scrubbing contaminated microbiomes. Nat Rev Microbiol 21, 554 (2023). https://doi.org/10.1038/s41579-023-00941-y

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  • DOI: https://doi.org/10.1038/s41579-023-00941-y

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