Batch effects account for the main findings of an in utero human intestinal bacterial colonization study
Abstract A recent study by Rackaityte et al. reported evidence for a low level of bacterial colonization, specifically of Micrococcus luteus, in the intestine of second trimester human fetuses. We have re-analyzed their sequence data and identified a batch effect which violates the underlying assump...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-01-01
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| Series: | Microbiome |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s40168-020-00949-z |
| _version_ | 1828939381102084096 |
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| author | Marcus C. de Goffau D. Stephen Charnock-Jones Gordon C. S. Smith Julian Parkhill |
| author_facet | Marcus C. de Goffau D. Stephen Charnock-Jones Gordon C. S. Smith Julian Parkhill |
| author_sort | Marcus C. de Goffau |
| collection | DOAJ |
| description | Abstract A recent study by Rackaityte et al. reported evidence for a low level of bacterial colonization, specifically of Micrococcus luteus, in the intestine of second trimester human fetuses. We have re-analyzed their sequence data and identified a batch effect which violates the underlying assumptions of the bioinformatic method used for contamination removal. This batch effect resulted in Micrococcus not being identified as a contaminant in the original work and being falsely assigned to the fetal samples. We further provide evidence that the micrographs presented by Rackaityte et al. are unlikely to show Micrococci or other bacteria as the size of the particles shown exceeds that of related bacterial cells. Finally, phylogenetic analysis showed that the microbes cultured from the fetal samples differed significantly from those detected by sequencing. Overall, our findings show that the presence of Micrococcus in the fetal gut is not supported by the primary sequence data. Our findings underline important aspects of the nature of contamination for both sequencing and culture approaches in microbiome studies and the appropriate use of automated contamination identification tools. |
| first_indexed | 2024-12-14T03:00:38Z |
| format | Article |
| id | doaj.art-933818bce3d840ed8c3f6b44c57ef1bd |
| institution | Directory Open Access Journal |
| issn | 2049-2618 |
| language | English |
| last_indexed | 2024-12-14T03:00:38Z |
| publishDate | 2021-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbiome |
| spelling | doaj.art-933818bce3d840ed8c3f6b44c57ef1bd2022-12-21T23:19:31ZengBMCMicrobiome2049-26182021-01-01911710.1186/s40168-020-00949-zBatch effects account for the main findings of an in utero human intestinal bacterial colonization studyMarcus C. de Goffau0D. Stephen Charnock-Jones1Gordon C. S. Smith2Julian Parkhill3Department of Veterinary Medicine, University of CambridgeDepartment of Obstetrics and Gynaecology, National Institute for Health Research Biomedical Research Centre, University of CambridgeDepartment of Obstetrics and Gynaecology, National Institute for Health Research Biomedical Research Centre, University of CambridgeDepartment of Veterinary Medicine, University of CambridgeAbstract A recent study by Rackaityte et al. reported evidence for a low level of bacterial colonization, specifically of Micrococcus luteus, in the intestine of second trimester human fetuses. We have re-analyzed their sequence data and identified a batch effect which violates the underlying assumptions of the bioinformatic method used for contamination removal. This batch effect resulted in Micrococcus not being identified as a contaminant in the original work and being falsely assigned to the fetal samples. We further provide evidence that the micrographs presented by Rackaityte et al. are unlikely to show Micrococci or other bacteria as the size of the particles shown exceeds that of related bacterial cells. Finally, phylogenetic analysis showed that the microbes cultured from the fetal samples differed significantly from those detected by sequencing. Overall, our findings show that the presence of Micrococcus in the fetal gut is not supported by the primary sequence data. Our findings underline important aspects of the nature of contamination for both sequencing and culture approaches in microbiome studies and the appropriate use of automated contamination identification tools.https://doi.org/10.1186/s40168-020-00949-zBatch effectsDecontamColonization in utero16S rRNA |
| spellingShingle | Marcus C. de Goffau D. Stephen Charnock-Jones Gordon C. S. Smith Julian Parkhill Batch effects account for the main findings of an in utero human intestinal bacterial colonization study Microbiome Batch effects Decontam Colonization in utero 16S rRNA |
| title | Batch effects account for the main findings of an in utero human intestinal bacterial colonization study |
| title_full | Batch effects account for the main findings of an in utero human intestinal bacterial colonization study |
| title_fullStr | Batch effects account for the main findings of an in utero human intestinal bacterial colonization study |
| title_full_unstemmed | Batch effects account for the main findings of an in utero human intestinal bacterial colonization study |
| title_short | Batch effects account for the main findings of an in utero human intestinal bacterial colonization study |
| title_sort | batch effects account for the main findings of an in utero human intestinal bacterial colonization study |
| topic | Batch effects Decontam Colonization in utero 16S rRNA |
| url | https://doi.org/10.1186/s40168-020-00949-z |
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