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Contrary to prevailing dogma, recent studies have indicated that the intrauterine environment may harbor commensal bacteria in the absence of adverse outcomes. We and others have profiled the microbiota associated with amniotic fluid and placenta of both preterm and healthy term pregnancies, but these observations have been mostly limited to the time of delivery. To determine if commensal bacteria could be detected earlier in gestation, we sought to profile the commensal microbiota associated with second trimester amniotic fluid samples obtained from genetic amniocentesis, and contrast it with the microbiota of other maternal body sites.
This was a prospective cohort study (n=95) that included amniotic fluid obtained from a genetic amniocentesis (gestational ages 16-20 wks). DNA from 500 ul of amniotic fluid was extracted (MoBio) and analyzed by 16S rRNA gene sequencing on the MiSeq platform (V4). Taxa identified in a negative kit control processed in parallel were considered contamination and subsequently filtered from downstream analysis. Remaining taxa were compared to previously published data of maternal ante- and intrapartum samples comprising multiple body niches.
After stringent filtering, 1685465 high quality reads were assigned to 635 unique taxa across 95 amniotic fluid samples (μ reads/sample = 17741, σ=11902). Consistent with our previous observations of the placental microbiome, the most prevalent taxa (90/95, 94.7%) belonged to the Escherichia, with an average abundance of 15.5% when present (Fig. A). However, the overall community structure of the amniotic fluid microbiome remained distinct from other body sites but bore the greatest similarity to the placenta (Fig. B) and oral cavity and nares (Fig. C, p<0.001).
We provide evidence of a distinct microbial community within the amniotic fluid as early as the second trimester, providing further supporting evidence for a non-sterile in utero environment. Interestingly, many of the taxa of the AF microbiota in the mid trimester were shared with that of the placenta interrogated at delivery. Further studies are warranted to determine the mechanisms through which microbiota can colonize the intrauterine space and its on obstetrical outcomes and fetal development.