Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
Department of Obstetrics and Gynaecology, National Institute for Health Research Biomedical Research Centre, University of Cambridge, Cambridge, UK.
Microbiome. 2021 Jan 12;9(1):6. doi: 10.1186/s40168-020-00949-z.
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.
拉凯蒂泰等人最近的一项研究报告称，在人类胎儿妊娠中期的肠道中，细菌定植水平较低，特别是微球菌属的微球菌。我们重新分析了他们的序列数据，发现了一个批次效应，该效应违反了用于去除污染的生物信息学方法的基本假设。该批次效应导致微球菌在原始工作中未被鉴定为污染物，而是被错误地分配到胎儿样本中。我们进一步提供的证据表明，拉凯蒂泰等人展示的显微照片不太可能显示微球菌或其他细菌，因为显示的颗粒大小超过了相关细菌细胞的大小。最后，系统发育分析表明，从胎儿样本中培养出的微生物与通过测序检测到的微生物有很大的不同。总的来说，我们的研究结果表明，胎儿肠道中存在微球菌的说法并没有得到原始序列数据的支持。我们的研究结果强调了微生物组研究中测序和培养方法污染的本质，以及自动化污染识别工具的正确使用。
