Abstract
Establishing a diverse gut microbiota after birth is being increasingly recognised as important for preventing illnesses later in life. It is well established that bacterial diversity rapidly increases post-partum; however, few studies have examined the infant gut virome/phageome during this developmental period. We performed a metagenomic analysis of 20 infant faecal viromes at one year of age to determine whether spontaneous vaginal delivery (SVD) or caesarean section (CS) influenced viral composition. We find that birth mode results in distinctly different viral communities, with SVD infants having greater viral and bacteriophage diversity. We demonstrate that CrAssphage is acquired early in life, both in this cohort and two others, although no difference in birth mode is detected. A previous study has shown that bacterial OTU’s (operational taxonomic units) identified in the same infants could not discriminate between birth mode at 12 months of age. Therefore, our results indicate that vertical transmission of viral communities from mother to child may play a role in shaping the early life microbiome, and that birth mode should be considered when studying the early life gut virome.
Highlights
The human gut microbiota is a diverse community densely populated with bacteria, archaea, protists, fungi, and viruses
Sequencing resulted in a mean of 924,917 paired end reads per sample, which dropped to 697,558 following strict quality control, making this the deepest sequenced infant virome dataset to date (Lim et al, 2015; Reyes et al, 2015)
Paired end sequence reads were classified against the nr database from NCBI using Kaiju (Menzel, Ng & Krogh, 2016) which translates reads into six possible read frames for classification based on amino acid homology (Fig. 1A)
Summary
The human gut microbiota is a diverse community densely populated with bacteria, archaea, protists, fungi, and viruses. Gut microbiota colonization in infants is a critical process, characterised by initial low bacterial diversity which increases with time such that by one year of age the microbiota converges towards that of an adult and fully resembles an adult microbiota. Several factors have been shown to influence an infant’s microbiota, from birth mode to antibiotic usage, diet, geographical location, lifestyle and age (Milani et al, 2017; Rodriguez et al, 2015). Hill et al (2017) confirmed that delivery mode and gestational age significantly influence bacterial composition in the infant gut during the first 24 weeks of life
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