Understanding the bacteriome, phageome and phage-associated bacteriome in healthy Vietnamese children under two years of age.

The establishment of the intestinal microbiota during early life plays an important role in physical and mental development and in shaping disease susceptibility in adult. However, knowledge of the gut microbiota in healthy Vietnamese children remains limited. In this study, real-time PCR was used to detect 24 diarrheal pathogens in stool samples, revealing that 41% of healthy infants aged 6-24 months living in Hanoi, Hung Yen were asymptomatic carriers of Escherichia coli (29.1%), Clostridioides difficile (10.3%) and Sapovirus. Pooled metagenomes of gut bacteria (HMG1, HMG2) and viruses (HV1, HV2) from two groups of pathogen-negative infants aged 6-11 months (n = 17) and 12-24 months (n = 13) were subsequently sequenced. As expected, from the classified reads, HMGs comprised of 99.99% bacterial reads, while HVs comprised of bacteria (78.5% in HV1, 42.3% in HV2), phages (8.3% in HV1, 41.0% in HV2) and viruses. The gut microbiota was formed by core bacteria: Actinobacteria (82.6-84.5%), Firmicutes, Proteobacteria and Bacteroidetes, with abundance of Bifidobacterium (> 80%), phages: Podoviridae (65.5-70.2%), Siphoviridae, Myoviridae with dominant crAssphage. The HMGs and HVs shared core bacterial composition but differed in relative abundance. The gut microbiota of older children was characterized by an increase of probiotic bacteria, Escherichia phage, Lactococcus phage and decrease of bacterial pathogens and phages targeting Lactobacillus, Klebsiella, Acinetobacter. Bacterial genes in the gut phage fraction may reflect bacterial community in recent past. Overall, this study provides a scientific basis for understanding the gut microbiome in relation to health and diseases in children particularly within the Vietnamese population.