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

41% of healthy infants aged 6-24 months were asymptomatic carriers of diarrheal pathogens.

• Real-time PCR was used to detect 24 diarrheal pathogens in stool samples from healthy infants in Hanoi and Hung Yen.
• Escherichia coli was the most prevalent pathogen, detected in 29.1% of infants.
• Clostridioides difficile was detected in 10.3% of infants.
• Sapovirus was also detected among the asymptomatic carriers.
• Children were aged 6-24 months and were clinically healthy (asymptomatic).

Pooled gut metagenomes from pathogen-negative infants were dominated by bacterial reads, while viral fraction metagenomes contained a substantial proportion of bacterial reads alongside phage reads.

• Two groups of pathogen-negative infants were sequenced: aged 6-11 months (n=17, HMG1/HV1) and 12-24 months (n=13, HMG2/HV2).
• From classified reads, HMGs (gut bacteria metagenomes) comprised 99.99% bacterial reads.
• Viral fraction metagenomes (HVs) contained bacteria at 78.5% in HV1 and 42.3% in HV2.
• Phage reads comprised 8.3% in HV1 and 41.0% in HV2.
• Pooled metagenomics sequencing was used for both bacteriome (HMG) and virome (HV) fractions.

The core gut bacteriome was dominated by Actinobacteria and Bifidobacterium across both age groups.

• Core bacteria consisted of Actinobacteria (82.6-84.5%), Firmicutes, Proteobacteria, and Bacteroidetes.
• Bifidobacterium accounted for more than 80% of the gut bacterial community.
• This composition was consistent across the two age groups (6-11 months and 12-24 months).
• HMGs and HVs shared core bacterial composition but differed in relative abundance.

The gut phageome was dominated by Podoviridae and crAssphage across both age groups.

• Podoviridae was the dominant phage family, comprising 65.5-70.2% of the phage community.
• Siphoviridae and Myoviridae were also identified as core phage families.
• crAssphage was the dominant phage within the community.
• This phage composition was observed across both the 6-11 month and 12-24 month age groups.

The gut microbiota of older children (12-24 months) showed age-related shifts compared to younger infants (6-11 months).

• Older children showed an increase in probiotic bacteria relative to younger infants.
• Escherichia phage and Lactococcus phage were increased in older children.
• Bacterial pathogens decreased in older children.
• Phages targeting Lactobacillus, Klebsiella, and Acinetobacter decreased in older children.
• These changes reflect maturation of the gut microbiota over the first two years of life.

Bacterial genes detected in the gut phage fraction may reflect the bacterial community composition from the recent past.

• Bacterial genetic material was found within the viral/phage fraction of the gut metagenome.
• The authors suggest this phage-associated bacteriome (bacterial reads in HV fractions) mirrors the recent bacterial community.
• Bacterial reads in HV1 comprised 78.5% and in HV2 comprised 42.3% of classified reads.
• This finding suggests the phage fraction can serve as an indirect record of past bacterial community states.