Viromes of one year old infants reveal the impact of birth mode on microbiome diversity

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Microbiology

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Introduction

Materials & Methods

Selection of faecal samples

Preparation of faecal viral suspensions

Extraction of viral DNA

Viral DNA amplification, library preparation and sequencing

Torque Teno Virus qPCR detection

Analysis of Virome Sequencing Data

Metagenomic analysis

Statistical analyses

Results & Discussion

Conclusion

Supplemental Information

Metadata of infant subjects subjects

Each row corresponds to a infant used in the study reporting their metadata and SRA accession number.

DOI: 10.7717/peerj.4694/supp-1

Number of reads per sample, alpha diversity values and estimates of human contamination per sample

DOI: 10.7717/peerj.4694/supp-2

Estimates of levels of 16S rRNA and cpn60 per sample for the Infant viromes in this study and Human Microbiome Project shotgun samples

DOI: 10.7717/peerj.4694/supp-3

Description of each assembled sequence used in the study

Table containing annotation for each assembled sequence used in this study - ID, top BLASTn hit in the nt database, circular, size, coverage.

DOI: 10.7717/peerj.4694/supp-4

Output of DESeq2 test for differentially abundant sequences between birth modes

Positive log fold changes represent an increase in C-section relative to SVD. The column padj corresponds to the p value adjusted for multiple testing.

DOI: 10.7717/peerj.4694/supp-5

The richness of Torque Teno Virus (TTV) ORF1 in each sample by breastfeeding status

Boxplot of the number of detectable homologues of Torque Teno Virus (TTV) ORF1 in each sample by breastfeeding status.

DOI: 10.7717/peerj.4694/supp-6

Heatplot of nucleotide identity across infant CrAssphage genomes

Heatplot demonstrating the level of nucleotide identity across the CrAssphage genomes assembled in this study, the original CrAssphage and from the Reyes et al., 2015 Malawi infant study.

DOI: 10.7717/peerj.4694/supp-7

Estimates of bacterial contamination

Percentage of 16S rRNA and cpn60 per sample in viromes sequenced in this study, as well as whole shotgun metagenomics samples from the Human Microbiome Project for comparsion.

DOI: 10.7717/peerj.4694/supp-8

Chao1 diversity for the virome and 16S rRNA INFANTMET data, stratified by birth mode

Each point represents the Chao1 diversity estimate based on the assembled sequences per infant faecal sample.

DOI: 10.7717/peerj.4694/supp-9

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Angela McCann analyzed the data, contributed reagents/materials/analysis tools.

Feargal J. Ryan analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Stephen R. Stockdale performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Marion Dalmasso performed the experiments, contributed reagents/materials/analysis tools.

Tony Blake analyzed the data.

C. Anthony Ryan, Catherine Stanton and Paul R. Ross conceived and designed the experiments.

Susan Mills authored or reviewed drafts of the paper.

Colin Hill conceived and designed the experiments, authored or reviewed drafts of the paper.

Human Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

The infants included in this study are part of the INFANTMET study cohort. Infant guardians were approached for written consent between February 2012 and May 2014 in Cork University Maternity Hospital, with ethical approval provided by the Cork University Hospital Research Ethics Committee.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

Sequence Read Archive:

PRJNA385126.

Data Availability

The following information was supplied regarding data availability:

The raw sequence data has been deposited in the NCBI Sequence Read Archive under the accession number SRP106048. Accession numbers for each individual subject are available in Table S1. FastQC reports, R code, assembled sequences, BLASTn output against the nt database, taxonomic assignments 16S sequences and count tables for both virome and 16S rRNA data were deposited in FigShare and are available at Ryan, Feargal (2018): INFANTMET Virome Study. figshare. Fileset. https://doi.org/10.6084/m9.figshare.5948443.v1

Funding

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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