Negativeome characterization and decontamination in early-life virome studies

Nataliia Kuzub, Alexander Kurilshikov, Alexandra Zhernakova and Sanzhima Garmaeva ()
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Nataliia Kuzub: University Medical Center Groningen
Alexander Kurilshikov: University Medical Center Groningen
Alexandra Zhernakova: University Medical Center Groningen
Sanzhima Garmaeva: University Medical Center Groningen

Nature Communications, 2025, vol. 16, issue 1, 1-12

Abstract: Abstract Contaminant sequences of external origin complicate the study of host-associated viromes, particularly in low-biomass samples obtained through viral-like particle (VLP) enrichment. However, the prevalence and impact of external contaminants on low-biomass samples are under-studied. Here, we analyze 1321 gut virome samples and 55 negative controls (NCs) from four early-life virome studies. Virus sequences identified in NCs, termed negativeome, were used as a proxy for the contamination assessment. We show that 61% of samples share at least one identical strain with negativeome, likely representing external contamination. While the median abundance of contaminant strains in these samples is only 1%, it ranges from 0 to 99% and exceeds 10% in 11% of infant samples. We further demonstrate that contamination is largely study-specific and has a greater impact on infant samples than on maternal samples. Based on our results, we propose a contamination assessment method using a publicly available database of sequences detected in NCs and a strain-level decontamination strategy.

Date: 2025
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DOI: 10.1038/s41467-025-61478-7

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