Reduced metagenomic sequencing (RMS) approach to determine the gut-associated phageome in mother-child

The role of the human gut phageome (HGP) for a healthy gut microbiome is not well-established. This study aims to identify phages based on Reduced Metagenome Sequencing (RMS) fragments from an Indian mother and child cohort. For this study, fecal samples were collected from 17 mother-infant pairs at Nishanth Hospital, Tamil Nadu, India. RMS data analysis and shotgun sequencing approaches were used to assemble and identify the genome fragments. Out of the 156,926 RMS fragments, 434 were classified as bacteriophages by Kraken 2. Mapping of virus sequences in NCBI and de novo assembly with subsequent taxonomic assignment revealed 41 different phage species. The prevalence (>50%) of three bacteriophages was observed in mother and child; overall four phages were more prevalent in the mothers while one phage was more prevalent in the children. Even at the species level, mothers were found to have more diverse phage species than children. No significant association was observed for mother–child sharing of phages. This study highlights the prevalence of Caudovirales phages in healthy HGP and also the use of the RMS approach to study the phageome composition.