Presence of distinctive microbiome in the first-pass meconium of newborn infants

Jenni Turunen,Outi Lindgren,Justus Reunanen,Niko Paalanne,Mika Kaakinen,Terhi Tapiainen,Tytti Pokka,Mysore V Tejesvi,Jenni Hekkala,Anna Kaisanlahti

doi:10.1038/s41598-021-98951-4

Jenni Turunen, Outi Lindgren + Show 8 more

Open Access

https://doi.org/10.1038/s41598-021-98951-4

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Journal: Scientific Reports	Publication Date: Sep 30, 2021
Citations: 17	License type: open-access

Affiliation: University of Oulu, Oulu University Hospital

Abstract

We critically evaluated the fetal microbiome concept in 44 neonates with placenta, amniotic fluid, and first-pass meconium samples. Placental histology showed no signs of inflammation. Meconium samples were more often bacterial culture positive after vaginal delivery. In next-generation sequencing of the bacterial 16S gene, before and after removal of extracellular and PCR contaminant DNA, the median number of reads was low in placenta (48) and amniotic fluid (46) and high in meconium samples (14,556 C-section, 24,860 vaginal). In electron microscopy, meconium samples showed extracellular vesicles. Utilizing the analysis of composition of microbiomes (ANCOM) against water, meconium samples had a higher relative abundance of Firmicutes, Lactobacillus, Streptococcus, and Escherichia-Shigella. Our results did not support the existence of the placenta and amniotic fluid microbiota in healthy pregnancies. The first-pass meconium samples, formed in utero, appeared to harbor a microbiome that may be explained by perinatal colonization or intrauterine colonization via bacterial extracellular vesicles.

Highlights

We critically evaluated the fetal microbiome concept in 44 neonates with placenta, amniotic fluid, and first-pass meconium samples
The fetal microbiome concept was developed after culture-independent methods, mainly next-generation sequencing of the bacterial 16S marker gene, had shown diverse microbiome signatures in the first-pass meconium formed in u tero[1,2,3], amniotic fluid1,3, placenta[1,4,5,6], and fetal lungs[7]
The first-pass meconium, appeared to harbor an actual microbiome, which may be explained by perinatal colonization, or hypothetically, partly by intrauterine colonization through bacterial extracellular vesicles, based on preliminary electron microscopy findings

Summary

Introduction

We critically evaluated the fetal microbiome concept in 44 neonates with placenta, amniotic fluid, and first-pass meconium samples. In next-generation sequencing of the bacterial 16S gene, before and after removal of extracellular and PCR contaminant DNA, the median number of reads was low in placenta (48) and amniotic fluid (46) and high in meconium samples (14,556 C-section, 24,860 vaginal). In order to critically investigate the proposed fetal microbiome concept further, we set out to characterize microbiomes in the first-pass meconium, placenta, and amniotic fluid; first, by next-generation sequencing of the bacterial 16S gene of unprocessed samples and after removal of extracellular bacterial DNA and contaminant bacterial DNA in PCR reagents. We investigated the histology of the placenta and performed bacterial culture and electron microscopy of the first stool to detect whole-cell bacteria or extracellular vesicles

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