Reply Re: “Amniotic fluid from healthy term pregnancies does not harbor a detectable microbial community”
How and when a newborn is first colonized by microbes continues to be of great interest due to its broad implications on human health and disease. Payne et al. express their opinion about our recent study in which we characterized the virome and bacterial microbiota of amniotic fluid from 24 uncomplicated term pregnancies. We conducted additional validation studies and respond to their comments. We conclude that in amniotic fluid from healthy term pregnancies, the bacterial microbiota is indistinguishable from contamination controls, and there is no evidence of a core virome.
How and when a newborn is first colonized by microbes continues to be of great interest due to its broad implications on human health and disease . Payne et al. express their opinion about our recent study in which we characterized the virome and bacterial microbiota of amniotic fluid from 24 uncomplicated term pregnancies. We failed to identify a population of bacterial microbiota which was statistically different in concentration or content from the sequences amplified in the negative controls. Additionally, we found sparse viral reads and no evidence for a core viral community across samples.
Payne et al. comment that our findings contradict two prior studies on the amniotic fluid bacterial microbiome [2, 3]. However, these studies have important distinctions from our study of healthy term pregnancies. First, Urushiyama et al. studied amniotic fluid from women with varying degrees of placental inflammation. A major conclusion from their study is that the microbial profile in amniotic fluid of Blanc’s classification stage III chorioamnionitis may have diagnostic applications . Chorioamnionitis, characterized by intrauterine inflammation or bacterial infection, has a vastly different placental histopathology and inflammatory cytokine microenvironment than healthy term pregnancies . Second, Collado et al. does not include similar negative controls to assess sample extraction and preparation contamination. Third, a recent study by Rehbinder et al. demonstrated that by culture, 16S rRNA gene quantification (digital droplet), and 16S rRNA sequencing, amniotic fluid obtained from term pregnancies in which membranes are not ruptured cannot be distinguished from negative controls . Therefore, taken together, maternal health likely has a major impact on the developing fetus’ first microbial exposure.
Payne et al. state that “the authors have only included OTUs in their analyses that originated from bacterial reads which were detected in the amniotic fluid samples and not in the blank extraction or PCR controls, regardless of the levels at which they were detected (Fig. 2)”. On the contrary, the data in the 16S rRNA gene analyses shown in Fig. 2a–c (OTU richness, diversity, and PCoA) of  includes all OTUs, not just those unique to amniotic fluid. Therefore, Fig. 2c of , in addition to Figure 1 of , shows that there is no statistically significant difference between the bacterial microbiota detected in amniotic fluid and buffer controls by either quantity or community content. As stated in the original study, subtraction of control-derived bacterial reads was only performed for the analysis shown in Fig. 2d of , which demonstrated the presence of low abundant rare bacterial OTUs unique to the amniotic fluid which were not frequently detected across the other amniotic fluid specimens.
In summary, our original paper , a recent publication from another group , and the data provided here converge on our original conclusions that “the most parsimonious explanation for our inability to find differences is that amniotic fluid of healthy term pregnancies has negligible bacterial biomass.” Further, “based on these analyses, we provisionally conclude that the term infant is not normally exposed to bacterial or viral populations in the immediate pre-birth interval”.
This work was supported in part by the Children’s Discovery Institute (MD-FR-2013-292), Doris Duke Charitable Foundation (2017076), March of Dimes (BOC 388999), the Women and Infant Health Consortium program at Washington University which is supported in part by the Washington University Institute of Clinical and Translational Sciences by the NIH/National Center for Advancing Translational Sciences (NCATS), CTSA grant UL1TR000448, NIH grant R00 DK107923 and Arizona State University startup funding (ESL).
Availability of data and materials
Sequence data from the original study has been deposited to the NCBI Sequence Read Archive under BioProject accession number SRP128680.
LRH and ESL conceived and designed the experiments, analyzed the data, and wrote the manuscript. CR performed the experiments. All authors read and approved the final manuscript.
Ethics approval and consent to participate
The institutional review board at Washington University School of Medicine approved the study. Subjects provided informed consent to be included in the Women and Infants Health Specimen Consortium biobank at Washington University.
Consent for publication
The authors declare that they have no competing interests.
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- 4.Gomez-Lopez N, Romero R, Maymon E, Kusanovic JP, Panaitescu B, Miller D, Pacora P, Tarca AL, Motomura K, Erez O, et al. Clinical chorioamnionitis at term IX: in vivo evidence of intra-amniotic inflammasome activation. J Perinat Med. 2018. https://doi.org/10.1515/jpm-2018-0271. [Epub ahead of print].
- 7.Lim ES, Rodriguez C, and Holtz LR. Correction to: Amniotic fluid from healthy term pregnancies does not harbor a detectable microbial community. Microbiome. 2019; https://doi.org/10.1186/s40168-019-0641-6.
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