Abstract
The short and long-term impact of birth mode on the developing gut microbiome in neonates has potential implications for the health of infants. In term infants, the microbiome immediately following birth across multiple body sites corresponds to birth mode, with increased Bacteroides in vaginally delivered infants. We aimed to determine the impact of birth mode of the preterm gut microbiome over the first 100 days of life and following neonatal intensive care unit (NICU) discharge. In total, 867 stool samples from 46 preterm infants (21 cesarean and 25 vaginal), median gestational age 27 weeks, were sequenced (V4 region 16S rRNA gene, Illumina MiSeq). Of these, 776 samples passed quality filtering and were included in the analysis. The overall longitudinal alpha-diversity and within infant beta-diversity was comparable between cesarean and vaginally delivered infants. Vaginally delivered infants kept significantly more OTUs from 2 months of life and following NICU discharge, but OTUs lost, gained, and regained were not different based on birth mode. Furthermore, the temporal progression of dominant genera was comparable between birth modes and no significant difference was found for any genera following adjustment for covariates. Lastly, preterm gut community types (PGCTs) showed some moderate differences in very early life, but progressed toward a comparable pattern by week 5. No PGCT was significantly associated with cesarean or vaginal birth. Unlike term infants, birth mode was not significantly associated with changes in microbial diversity, composition, specific taxa, or overall microbial development in preterm infants. This may result from the dominating effects of NICU exposures including the universal use of antibiotics immediately following birth and/or the lack of Bacteroides colonizing preterm infants.
Highlights
Following birth, a neonate encounters large numbers of viable microbes
We investigated the longitudinal development of the microbiome during the first 100 days of life and following discharge
In a large meta-analysis of preterm gut microbiome, infants delivered by cesarean section had increased Firmicutes and reduced Bacteroides, but the overall microbiome profiles were comparable (Pammi et al, 2017)
Summary
Following birth, a neonate encounters large numbers of viable microbes. Despite emerging evidence suggesting the potential for prenatal exposure to microorganisms during the fetal stages (Jiménez et al, 2008; Aagaard et al, 2014; Collado et al, 2016), the main colonisation event occurs at birth, where for term infants birth mode shapes what microbes are passed from the mother to the offspring (Aagaard et al, 2016). In infants delivered at term, the impact of birth mode has been studied in several longitudinal studies, most showing infants delivered vaginally have increased Bacteroides throughout the 1st year of life (Azad et al, 2013; Jakobsson et al, 2014; Bäckhed et al, 2015; Bokulich et al, 2016; Yassour et al, 2016) Contrary to these reports, no difference in the overall microbial community or in specific taxa between vaginal and cesarean infants at 6 weeks of life has been reported (Chu et al, 2017). Differences between cohorts and methods (e.g., sequencing depth) may account for these discrepancies
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