Background: The human microbiome includes trillions of bacteria, many of which play a vital role in host physiology. Numerous studies have now detected bacterial DNA in first-pass meconium and amniotic fluid samples, suggesting that the human microbiome may commence in-utero. However, these data have remained contentious due to underlying contamination issues.
Method: Here, we have used a novel method for reducing contamination in microbiome workflows to determine if there is a fetal bacterial microbiome beyond the level of background contamination. We recruited 50 women undergoing elective caesarean section with no evidence of intra-uterine infection and collected first-pass meconium and amniotic fluid samples. Full-length 16S rRNA gene sequencing was performed using PacBio SMRT cell CCS technology, to allow high resolution profiling of the fetal gut and amniotic fluid bacterial microbiomes. Levels of inflammatory cytokines were measured in amniotic fluid, and levels of immunomodulatory short chain fatty acids (SCFAs) were quantified in meconium. Propidium monoazide (PMA) was used to test the viability of bacteria detected in meconium samples.
Results: All meconium samples and most amniotic fluid samples (84%) contained bacterial DNA. Meconium contains a low diversity and low-biomass microbiome, which was remarkably variable between patients. Importantly, PMA testing confirmed that this community consisted of viable bacterial cells. The amniotic fluid microbiome was more diverse and contained mainly reads that mapped to typical skin commensals. All meconium samples contained acetate and propionate, at ratios similar to those previously reported in infants. Neonates born from mothers with Type 2 diabetes had significantly lower levels of propionate in their meconium compared to those born from mothers with normal pancreatic function (P=0.005) or from mothers with gestational diabetes (P=0.003). These differences were not associated with alterations in the fetal microbiome, suggesting that they may be driven by the maternal microbiome.
Conclusions: Our results demonstrate that viable bacterial cells and SCFAs are present in-utero, and have the potential to influence the developing fetus.