Is there a placental microbiota? A critical review and re-analysis of published placental microbiota datasets

Abstract

The existence of a placental microbiota is under debate. The human placenta has historically been considered sterile and microbial colonization has been associated with adverse pregnancy outcomes. Yet, recent investigations using DNA sequencing reported a microbiota in human placentas from typical term pregnancies. However, this detected microbiota could represent background DNA contamination. Using fifteen publicly available 16S rRNA gene datasets, existing data were uniformly re-analyzed. 16S rRNA gene Amplicon Sequence Variants (ASVs) identified as Lactobacillus were highly abundant in eight of fifteen studies. However, the prevalence of Lactobacillus, a typical vaginal bacterium, was clearly driven by bacterial contamination from vaginal delivery and background DNA. After removal of likely DNA contaminants, Lactobacillus ASVs were highly abundant in only one of five studies for which data analysis could be restricted to placentas from term cesarean deliveries. A six study sub-analysis targeting the 16S rRNA gene V4 hypervariable region demonstrated that bacterial profiles of placental samples and technical controls share principal bacterial ASVs and that placental samples clustered primarily by study origin and mode of delivery. Across studies, placentas from typical term pregnancies did not share a consistent bacterial taxonomic signal. Contemporary DNA- based evidence does not support the existence of a placental microbiota. IMPORTANCEEarly-gestational microbial influences on human development are unclear. By applying DNA sequencing technologies to placental tissue, bacterial DNA signals were observed, leading some to conclude that a live bacterial placental microbiome exists in typical term pregnancy. However, the low-biomass nature of the proposed microbiome and high sensitivity of current DNA sequencing technologies indicate that the signal may alternatively derive from environmental or delivery-associated bacterial DNA contamination. Here we address these alternatives with a re- analysis of 16S rRNA gene sequencing data from 15 publicly available placental datasets. After identical DADA2 pipeline processing of the raw data, subanalyses were performed to control for mode of delivery and environmental DNA contamination. Both environment and mode of delivery profoundly influenced the bacterial DNA signal from term-delivered placentas. Aside from these contamination-associated signals, consistency was lacking across studies. Thus, placentas delivered at term are unlikely to be the original source of observed bacterial DNA signals.