Negativeome characterization and decontamination in early-life virome studies
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...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-07-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-61478-7 |
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| author | Nataliia Kuzub Alexander Kurilshikov Alexandra Zhernakova Sanzhima Garmaeva |
| author_facet | Nataliia Kuzub Alexander Kurilshikov Alexandra Zhernakova Sanzhima Garmaeva |
| author_sort | Nataliia Kuzub |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-a4cb457fd307400a902a4031f2335570 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-a4cb457fd307400a902a4031f23355702025-08-20T03:45:33ZengNature PortfolioNature Communications2041-17232025-07-0116111210.1038/s41467-025-61478-7Negativeome characterization and decontamination in early-life virome studiesNataliia Kuzub0Alexander Kurilshikov1Alexandra Zhernakova2Sanzhima Garmaeva3Department of Genetics, University of Groningen, University Medical Center GroningenDepartment of Genetics, University of Groningen, University Medical Center GroningenDepartment of Genetics, University of Groningen, University Medical Center GroningenDepartment of Genetics, University of Groningen, University Medical Center GroningenAbstract 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.https://doi.org/10.1038/s41467-025-61478-7 |
| spellingShingle | Nataliia Kuzub Alexander Kurilshikov Alexandra Zhernakova Sanzhima Garmaeva Negativeome characterization and decontamination in early-life virome studies Nature Communications |
| title | Negativeome characterization and decontamination in early-life virome studies |
| title_full | Negativeome characterization and decontamination in early-life virome studies |
| title_fullStr | Negativeome characterization and decontamination in early-life virome studies |
| title_full_unstemmed | Negativeome characterization and decontamination in early-life virome studies |
| title_short | Negativeome characterization and decontamination in early-life virome studies |
| title_sort | negativeome characterization and decontamination in early life virome studies |
| url | https://doi.org/10.1038/s41467-025-61478-7 |
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