Genetics and Genomic Medicine, UCL GOS Institute of Child Health, UCL, London, United Kingdom
Microbiology, Virology and Infection Control, Great Ormond Street Hospital, NHS Foundation Trust, London, United Kingdom.
Appl Environ Microbiol. 2018 Jul 2;84(14). doi: 10.1128/AEM.00483-18. Print 2018 Jul 15.
In this study, differences in the placental microbiota from term and preterm deliveries in a large pregnancy cohort in the United Kingdom were studied by using 16S-targeted amplicon sequencing. The impacts of contamination from DNA extraction, PCR reagents, and the delivery itself were also examined. A total of 400 placental samples from 256 singleton pregnancies were analyzed, and differences between spontaneous preterm-, nonspontaneous preterm-, and term-delivered placentas were investigated. DNA from recently delivered placentas was extracted, and screening for bacterial DNA was carried out by using targeted sequencing of the 16S rRNA gene on the Illumina MiSeq platform. Sequenced reads were analyzed for the presence of contaminating operational taxonomic units (OTUs) identified via sequencing of negative extraction and PCR-blank samples. Differential abundances and between-sample (beta) diversity metrics were then compared. A large proportion of the reads sequenced from the extracted placental samples mapped to OTUs that were also found for negative extractions. Striking differences in the compositions of samples were also observed, according to whether the placenta was delivered abdominally or vaginally, providing strong circumstantial evidence for delivery contamination as an important contributor to observed microbial profiles. When OTU- and genus-level abundances were compared between the groups of interest, a number of organisms were enriched in the spontaneous preterm-delivery cohort, including organisms that have been associated previously with adverse pregnancy outcomes, specifically spp. and spp. However, analyses of the overall community structure did not reveal convincing evidence for the existence of a reproducible "preterm placental microbiome." Preterm birth is associated with both psychological and physical disabilities and is the leading cause of infant morbidity and mortality worldwide. Infection is known to be an important cause of spontaneous preterm birth, and recent research has implicated variation in the "placental microbiome" in the risk of preterm birth. Consistent with data from previous studies, the abundances of certain clinically relevant species differed between spontaneous preterm- and nonspontaneous preterm- or term-delivered placentas. These results support the view that a proportion of spontaneous preterm births have an intrauterine-infection component. However, an additional observation from this study was that a substantial proportion of sequenced reads were contaminating reads rather than DNA from endogenous, clinically relevant species. This observation warrants caution in the interpretation of sequencing outputs from low-biomass samples such as the placenta.
在这项研究中，通过使用 16S 靶向扩增子测序，研究了英国一个大型妊娠队列中足月和早产分娩的胎盘微生物组差异。还研究了 DNA 提取、PCR 试剂和分娩本身的污染影响。总共分析了 256 例单胎妊娠的 400 个胎盘样本，并研究了自发性早产、非自发性早产和足月分娩胎盘之间的差异。从最近分娩的胎盘中提取 DNA，并通过在 Illumina MiSeq 平台上对 16S rRNA 基因进行靶向测序来进行细菌 DNA 的筛选。对测序的阴性提取和 PCR 空白样本中鉴定的污染操作分类单元 (OTU) 的存在进行了测序读取分析。然后比较了差异丰度和样本间（β）多样性指标。从提取的胎盘样本中测序的大量reads 与从阴性提取物中发现的 OTUs 相对应。还观察到根据胎盘是经腹部还是经阴道分娩，样本的组成存在明显差异，这为分娩污染是观察到的微生物特征的重要贡献者提供了有力的间接证据。当在感兴趣的组之间比较 OTU 和属水平的丰度时，一些生物体在自发性早产分娩队列中富集，包括先前与不良妊娠结局相关的生物体，特别是 spp. 和 spp. 然而，对整体群落结构的分析并没有为存在可重复的“早产胎盘微生物组”提供令人信服的证据。早产与心理和身体残疾有关，是全球婴儿发病率和死亡率的主要原因。众所周知，感染是自发性早产的重要原因，最近的研究表明“胎盘微生物组”的变异与早产风险有关。与以前的研究数据一致，某些临床相关物种的丰度在自发性早产和非自发性早产或足月分娩的胎盘中有所不同。这些结果支持这样一种观点，即一部分自发性早产分娩具有宫内感染成分。然而，这项研究的另一个观察结果是，大量测序reads 是污染reads，而不是来自内源性、临床相关物种的 DNA。这一观察结果在解释胎盘等低生物量样本的测序结果时需要谨慎。
