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 — ontology label: Viruses | NCBITaxon:10239 · TaxonMech · TraitMech | N/A | |
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| infant Bacteroides hosts — ontology label: Bacteroides | NCBITaxon:816 · TaxonMech · TraitMech | N/A | |
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Ecological Interactions
The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.
Maternal Phage Sharing and Persistence Association
Strain-resolved metagenomes associate maternal sharing with infant phage persistence. The 155 of 1801 early phages classified as persisters came from the 40 infants with adequate follow-up; the roughly 9 percent is not a persistence rate for every maternally shared phage or Bacteroides host. Maternal classification uses sharing in early mother-infant samples. Predicted hosts and temperate lifestyles do not establish universal lytic predation. The canonical participants represent a maternal/Bacteroides-associated subset of the broader phage cohort, not all measured phages.
Participating Taxa: maternally transmitted DNA bacteriophages, infant Bacteroides hosts
PARTIAL - maternally shared phages may be adapted to the gut or repeatedly introduced, supporting subsequent strain persistence. The longitudinal sharing association supports this model but does not isolate maternal transmission, reseeding or infection direction experimentally.
Evidence
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PMID:38096814 - SUPPORT (IN_VIVO)"early phage colonizers, which are mostly maternally transmitted and infect Bacteroides, persist for 3 years"
Stop-Codon Reassignment and Phage Persistence Association
Phages with predicted stop-codon reassignment were more likely to persist. Of ten early recoded phages, three persisted and were maternally shared; only one of these had an identified Bacteroides vulgatus host. Longitudinal TAG changes differed among the three, including decreases, and do not show a universal increase. Proposed delayed lysis or host adaptation was not selectively tested. The canonical maternal-phage entry denotes the represented persister subset, not all viruses or all recoded phages.
Participating Taxa: maternally transmitted DNA bacteriophages
Biological Processes:
- viral process (GO:0016032 · PathwayMech)
PARTIAL - stop-codon reassignment could alter phage expression or lysis timing and thereby support persistence. Enrichment among persisters and heterogeneous sequence trajectories support the proposed mechanism, not a recoding perturbation demonstrating its necessity or sufficiency.
Evidence
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PMID:38096814 - SUPPORT (IN_VIVO)"phages with stop codon reassignment are more likely to persist than non-recoded phages"
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PMID:38096814 - PARTIAL (IN_VIVO)"an increase in in-frame reassigned stop codons over 3 years"
Increasing Phageome Richness Toward Adulthood
The cohort phageome becomes richer and reaches adult-like community complexity by age three. This positive community-level diversity observation is different from nucleotide diversity within an individual persistent phage population. It does not show that increasing richness causes a particular early phage strain to persist. The canonical maternal-phage entry is a represented subset, not the complete richness-assay roster.
Participating Taxa: maternally transmitted DNA bacteriophages
Biological Processes:
- viral process (GO:0016032 · PathwayMech)
Evidence
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PMID:38096814 - SUPPORT (IN_VIVO)"early-life phageome richness increases over time and reaches adult-like complexity by age 3"
Persistent Infant Phage Strains
In the longitudinal cohort, 155 of 1801 early phages met the persistence criterion among 40 infants with adequate follow-up; persistence was more frequent in full-term infants. Strain comparisons used 99 percent population ANI over at least 75 percent of compared genome sequence, distinct from the bacterial study threshold. Maternal sharing, recoding, predicted hosts and host CRISPR-Cas profiles inform proposed persistence mechanisms, not a jointly isolated causal model. The Bacteroides/maternal canonical participants are a supported subset, not all cohort hosts or phages. Co-detection and coverage correlations do not prove continuous infection of one unchanged host lineage.
Participating Taxa: maternally transmitted DNA bacteriophages, infant Bacteroides hosts
Biological Processes:
- viral process (GO:0016032 · PathwayMech)
Evidence
-
PMID:38096814 - SUPPORT (IN_VIVO)"9% of early phage colonizers, which are mostly maternally transmitted and infect Bacteroides, persist for 3 years"
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which proposed mechanisms causally maintain the observed infant phage strains?
Keep the maternal-sharing and recoding routes as partial models, not experimentally isolated determinants. Remove the richness arrow: community alpha diversity is not within-phage nucleotide diversity. Maternal bidirectional reseeding, host assignment, CRISPR-associated strain replacement and predicted temperate/lytic lifestyles remain distinct hypotheses or observations. Recoding trajectories are heterogeneous. Full primary main text, STAR Methods, four figure captions and two main tables read; no figure pixels, external supplements, raw data or code audited. Canonical taxonomy and non-graph fields are preserved, not recertified.
Attaches to: ecological_interactions#Maternal Phage Sharing and Persistence Association, ecological_interactions#Stop-Codon Reassignment and Phage Persistence Association, ecological_interactions#Increasing Phageome Richness Toward Adulthood, ecological_interactions#Persistent Infant Phage Strains
External Resources
| Name | Repository | Resource ID |
|---|---|---|
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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 |
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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 |
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| Host CRISPR-Cas locus prevalence | maternal seeding plus CRISPR-Cas and stop-codon recoding | N/A |
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