Metagenomic Analysis of the Gastrointestinal Phageome and Incorporated Dysbiosis in Children with Persistent Diarrhea of Unknown Etiology in Vietnam

Persistent diarrhea of unknown etiology in children under 2 years of age is a common problem and poses a major challenge for the health sector. However, knowledge of the composition and dysbiosis of the intestinal phageome, phage-associated bacteriome in the persistent diarrhea remains limited. In this study, a process for phage enrichment and metagenomic extraction was developed and applied to recover gut phage metagenomes from 30 healthy children and 30 children with persistent diarrhea for high-throughput sequencing. Taxonomic annotation using Kraken2 revealed that, besides <i>Norwalk virus</i>, <i>Primate bocaparvovirus 1</i> and <i>Human-associated gemykibivirus 2</i>, phage communities in the diarrhea group showed reduced diversity and contained sample-dependent phages targeting <i>Salmonella enterica</i>, <i>Enterobacter</i>, <i>Shigella flexneri</i>, <i>Clostridioides difficile</i>, <i>Pseudomonas aeruginosa</i>, <i>Streptococcus miti</i>, uropathogenic <i>Escherichia coli</i> and functioned balancing bacterial communities. Bacterial fraction in the metagenomic datasets reflected clear patterns of dysbiosis, including a severe deficiency of beneficial bacteria, an increase in Firmicutes, a marked decline in Actinobacteria, Bacteroidetes, Proteobacteria and sample-dependent enrichment of <i>Enterococcus</i>, <i>Escherichia</i> and <i>Acinetobacter</i> in diarrhea cases. This study, for the first time, investigated the dynamics of gut phageome, phage-associated bacteriome in children with persistent diarrhea of unknown causes in Vietnam, providing new insight for complementary treatment.