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Infant Gut DNA Phageome Succession Community

Community ID CommunityMech:000223
Ecological State STABLE
Environment infant gut microbiome
ENVO:00002009

A longitudinal infant gut DNA bacteriophage community reconstructed from 819 fecal metagenomes from 28 full-term and 24 preterm infants and their mothers across the first 3 years of life, using a large phage sequence database and strain-resolved analyses. Early-life phageome richness increases over time and reaches adult-like complexity by age 3. Approximately 9 percent of early phage colonizers persist for 3 years and are predominantly maternally transmitted phages infecting Bacteroides, with higher persistence in full-term infants. Phages with stop-codon reassignment are more likely to persist than non-recoded phages, and in-frame reassigned stop codons increase over the 3-year window. Maternal seeding, stop-codon reassignment, host CRISPR-Cas locus prevalence, and phage diversity together drive stable viral colonization.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
maternally transmitted DNA bacteriophages NCBITaxon:10239 N/A
  • PMID:38096814 - SUPPORT (IN_VIVO)
    "9% of early phage colonizers, which are mostly maternally transmitted and infect Bacteroides, persist for 3 years"
infant Bacteroides hosts NCBITaxon:816 N/A
  • PMID:38096814 - SUPPORT (IN_VIVO)
    "early phage colonizers, which are mostly maternally transmitted and infect Bacteroides"

Ecological Interactions

Ecological interaction network for Infant Gut DNA Phageome Succession Community Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).
Taxon
Cross-feeding
Mutualism
Syntrophy
Competition
Commensalism
Niche partitioning
Colonization facilitation
Strain competition
Predation

Maternal Phage Seeding and Long-Term Persistence

PREDATION

Source Taxon: maternally transmitted DNA bacteriophages

Target Taxon: infant Bacteroides hosts

Biological Processes:

Evidence

  • PMID:38096814 - SUPPORT (IN_VIVO)
    "early phage colonizers, which are mostly maternally transmitted and infect Bacteroides, persist for 3 years"

Stop-Codon Reassignment Promotes Phage Persistence

PREDATION

Evidence

  • PMID:38096814 - SUPPORT (IN_VIVO)
    "phages with stop codon reassignment are more likely to persist than non-recoded phages"
  • PMID:38096814 - SUPPORT (IN_VIVO)
    "an increase in in-frame reassigned stop codons over 3 years"

Increasing Phageome Richness Toward Adulthood

COLONIZATION_FACILITATION

Evidence

  • PMID:38096814 - SUPPORT (IN_VIVO)
    "early-life phageome richness increases over time and reaches adult-like complexity by age 3"

External Resources

Name Repository Resource ID
Primary publication for the infant gut DNA phageome succession community
PubMed record for the Lou et al. 2024 Cell Host & Microbe paper. 		OTHER PMID:38096814
  • PMID:38096814 - SUPPORT (IN_VIVO)
    "phage colonization process in the infant gut"
DOI landing page
DOI link to the Cell Host & Microbe paper. 		OTHER doi:10.1016/j.chom.2023.11.015

Environmental Factors

Factor Value Unit
Birth status full-term versus preterm infants N/A
  • PMID:38096814 - SUPPORT (IN_VIVO)
    "more prevalent in full-term than in preterm infants"
Host CRISPR-Cas locus prevalence maternal seeding plus CRISPR-Cas and stop-codon recoding N/A
  • PMID:38096814 - SUPPORT (IN_VIVO)
    "maternal seeding, stop codon reassignment, host CRISPR-Cas locus prevalence, and diverse phage populations contribute to stable viral colonization"