Rotavirus Vaccine Immunogenicity (RoVI) shotgun metagenomics

This project is a sub-study of the RoVI project, and contains shotgun metagenomic sequencing data with human reads removed. This extends the parent RoVI project (PRJEB38948) – a prospective observational cohort study which used 16S metataxonomic sequencing to perform within-country and between-country comparisons of gut microbiome composition among infants in India, Malawi, and the UK. Shotgun metagenomic data under the current accession were generated to provide a high-resolution taxonomic analysis of stool samples collected at 6 weeks of age, among a subset of infants in India and Malawi. Adapter sequences were removed from reads using Cutadapt version 1.2.1, trimming the 3' end of any reads which match the adapter sequence for 3 bp or more. Sickle version 1.200 was then used for further trimming of reads, with a minimum window quality score of 20. Any reads shorter than 15 bp after trimming were removed. Human DNA was removed from all paired-end reads by using the MetaWRAP read_qc module to align to the T2T consortium complete human genome, (GCF_009914755.1) and human mitochondrial genome (NC_012920.1). We then analysed the functional capacity of the developing microbiome in these cohorts. Microbiome composition differed significantly between countries, although functional capacity was more similar than taxonomic composition. Our results confirmed previously reported findings that the developing microbiome is more diverse in taxonomic composition in oral rotavirus vaccine non-seroconverters, compared with seroconverters. We additionally demonstrate a similar pattern in functional capacity. Previous publications have provided additional details on the RoVI study protocol (doi: 10.1136/bmjopen-2017-016577) and primary outcomes (doi: 10.1038/s41467-021-27074-1).