The human primordial microbiome hosts complex bacterial and fungal interkingdom ecologies that vary with gestational age

Abstract

Commensal microbial communities play important roles in human development. While microorganisms appear to be predominately transmitted from mother to child, the timing of transmission remains controversial. Meconium, the first stool passed after birth, was traditionally considered sterile because it originated from a sterile uterine environment. Following advances in next‐generation sequencing (NGS) techniques, more recent evidence suggests bacterial communities may exist in the gut prior to birth, however, the presence of primordial fungal communities has not been described. Here, we demonstrate the presence of multi‐kingdom microbial communities in meconium immediately following birth based on NGS. To describe the ecology of the primordial microbiome, we prospectively enrolled premature (gestational age < 32 weeks') very low birthweight (VLBW < 1500 g) and full term (FT, gestational age 37–41 weeks') newborns and collected the initial meconium. We examined the interkingdom community structure using 16S and ITS rDNA‐based amplicon sequencing followed by culture‐based techniques. We prospectively enrolled 57 VLBW and 35 FT newborns and collected a stool sample at < 48h of life from 34 infants in each group. Bacteria were found in meconium of 90% of VLBW and 82% of FT samples (χ2P=0.325) and fungi in 93% of VLBW and 62% of FT samples (χ2P=0.003). The bacterial and fungal communities differed significantly between VLBW and FT (bacteria: PERMANOVA P=0.006, fungi: PERMANOVA P=0.013). Fungal communities of VLBWs were dominated by Ascomycota, including Candida, while FT meconium contained greater Basidiomycota and taxonomic diversity. Bacterial communities in VLBW meconium were also less diverse and contained on average a third as many taxa compared with FT. These results demonstrate human meconium contains complex interkingdom microbial communities that develop with gestational age, suggesting host‐microbe interkingdom relationships may exist in the uterine environment. Intriguingly, fungi are 50% more commonly observed in premature meconium than in full term neonates which could suggest a pathological association with preterm birth.Support or Funding InformationThe Marshall Klaus Perinatal Research Award from the American Academy of PediatricsThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.