Author Identifier

Mary Boyce Orcid:

Document Type

Journal Article

Publication Title

Frontiers in Microbiology





PubMed ID





Centre for Integrative Metabolomics and Computational Biology / School of Science




LS is supported by an Australian Postgraduate Award from The University of Western Australia and an additional scholarship from the Women and Infants Research Foundation of Western Australia (WIRF). MP is supported by a National Health and Medical Research Council Project Grant (APP1077931) and JK is supported, in part, by WIRF. Funding for this research was provided by WIRF in the form of a Capacity Building Grant held by MP and a Channel 7 Telethon Trust grant awarded to JK.

Grant Number

NHMRC Number : 1077931


Stinson, L. F., Boyce, M. C., Payne, M. S., & Keelan, J. A. (2019). The not-so-sterile womb: Evidence that the human fetus is exposed to bacteria prior to birth. Frontiers in microbiology, 10, Article 1124. Available here


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. Here, we have used a previously described 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 non-emergency cesarean section deliveries 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 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. All meconium samples and most amniotic fluid samples (36/43) contained bacterial DNA. The meconium microbiome was dominated by reads that mapped to Pelomonas puraquae. Aside from this species, the meconium microbiome was remarkably heterogeneous between patients. The amniotic fluid microbiome was more diverse and contained mainly reads that mapped to typical skin commensals, including Propionibacterium acnes and Staphylococcus spp. All meconium samples contained acetate and propionate, at ratios similar to those previously reported in infants. P. puraquae reads were inversely correlated with meconium propionate levels. Amniotic fluid cytokine levels were associated with the amniotic fluid microbiome. Our results demonstrate that bacterial DNA and SCFAs are present in utero, and have the potential to influence the developing fetal immune system.



Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.