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, 6, e4694
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Viromes of One Year Old Infants Reveal the Impact of Birth Mode on Microbiome Diversity

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Viromes of One Year Old Infants Reveal the Impact of Birth Mode on Microbiome Diversity

Angela McCann et al. PeerJ.

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.

Keywords: Bacteriophage; Birth mode; Infant; Metagenomics; Microbiome; Virome.

Conflict of interest statement

The authors declare there are no competing interests.

Figures

Figure 1
Figure 1. Classification and abundance of known viral groups in the INFANTMET cohort.
(A) Log relative abundance of classifiable viral groups by the Kaiju amino acid classifier against the NR protein database. (B) Boxplot of the number of detectable homologues of Torque Teno Virus (TTV) ORF1 in each sample by birth mode. (C) Visualized alignment of multiple CrAssphage genomes of infant origin.
Figure 2
Figure 2. Alpha and beta diversity measures for virome and 16S rRNA sequence data in the INFANTMET cohort.
PCoAs of unweighted Bray–Curtis distances for the (A) virome and (B) 16S rRNA sequence datasets, respectively. Boxplots of Shannon diversity in the (C) virome and (D) 16S rRNA sequence datasets, respectively.

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References

    1. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–2120. doi: 10.1093/bioinformatics/btu170. - DOI - PMC - PubMed
    1. Breitbart M, Haynes M, Kelley S, Angly F, Edwards RA, Felts B, Mahaffy JM, Mueller J, Nulton J, Rayhawk S, Rodriguez-Brito B, Salamon P, Rohwer F. Viral diversity and dynamics in an infant gut. Research in Microbiology. 2008;159:367–373. doi: 10.1016/j.resmic.2008.04.006. - DOI - PubMed
    1. Breitbart M, Hewson I, Felts B, Mahaffy JM, Nulton J, Salamon P, Rohwer F. Metagenomic analyses of an uncultured viral community from human feces. Journal of Bacteriology. 2003;185:6220–6223. doi: 10.1128/JB.185.20.6220-6223.2003. - DOI - PMC - PubMed
    1. Coordinators NR Database resources of the national center for biotechnology information. Nucleic Acids Research. 2016;44:D7–D19. doi: 10.1093/nar/gkv1290. - DOI - PMC - PubMed
    1. Dutilh BE, Cassman N, McNair K, Sanchez SE, Silva GGZ, Boling L, Barr JJ, Speth DR, Seguritan V, Aziz RK, Felts B, Dinsdale EA, Mokili JL, Edwards RA. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nature Communications. 2014;5:4498. doi: 10.1038/ncomms5498. - DOI - PMC - PubMed

Grant support

The APC Microbiome Institute is a research centre funded by Science Foundation Ireland (SFI), through the Irish Government’s National Development Plan (Grant Number 12/RC/2273). The INFANTMET project was funded by the Irish Department of Agriculture, Food and Marine. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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