A longitudinal infant gut bacterial community studied at strain resolution over the first year of life across 13 full-term and 9 preterm infants and 17 mother-infant pairs. Infants' initially distinct microbiomes converge by age 1 year. Approximately 11 percent of early colonizers, primarily Bacteroides and Bifidobacterium, persist through the first year and are more prevalent in full-term than in preterm infants. Maternal gut strains are significantly more likely to persist in the infant gut than other strains. Enrichment in genes for surface adhesion, iron acquisition, and carbohydrate degradation may explain why some strains persist through the first year of life.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| persistent infant Bacteroides colonizers — ontology label: Bacteroides | NCBITaxon:816 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
CROSS_FEEDER
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ABUNDANT |
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| persistent infant Bifidobacterium colonizers — ontology label: Bifidobacterium | NCBITaxon:1678 · TaxonMech · TraitMech |
CROSS_FEEDER
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ABUNDANT |
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| maternal-origin gut bacterial strains — ontology label: Bacteria | NCBITaxon:2 · TaxonMech · TraitMech |
CROSS_FEEDER
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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 Strain Sharing and Persistence Association
Among 17 mother-infant pairs, maternal strain sharing was associated with subsequent infant persistence. Maternal transmission was particularly enriched among Bacteroides, whereas persistent Bifidobacterium strains often lacked a maternal match. Sharing supports maternal-origin association, not a selectively established dominant driver or repeated reseeding mechanism. The canonical Bacteria entry represents the sampled maternal-origin strain class, not a property of all bacteria.
Participating Taxa: maternal-origin gut bacterial strains
PARTIAL - maternal gut adaptation or repeated introduction could support infant retention of shared strains, particularly the Bacteroides-enriched maternal subset. The observational association does not isolate either mechanism or explain all Bifidobacterium persisters.
Evidence
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PMID:34622230 - SUPPORT (IN_VIVO)"maternal gut strains are significantly more likely to persist in the infant gut than other strains"
Bifidobacterium Persister Carbohydrate-Gene Enrichment
Within-genus comparison of 12 Bifidobacterium persisters and 18 non-persisters found higher CAZyme diversity and coding density in persister genomes. This is positive genomic association, not measured expression, enzyme activity or demonstrated commensalism. The separate E. coli comparison used three persisters and 25 non-persisters; its iron-acquisition and adhesion findings cannot be assigned to the canonical Bacteroides or Bifidobacterium entries. Exact E. coli representation and broader trait structure remain unresolved under #1515.
Participating Taxa: persistent infant Bifidobacterium colonizers
Biological Processes:
- carbohydrate metabolic process (GO:0005975 · PathwayMech)
PARTIAL - a broader encoded carbohydrate repertoire could support substrate use and persistence of Bifidobacterium strains within the downstream persister group. Within-genus enrichment supports this hypothesis, not measured enzyme flux or necessity, and does not assign E. coli iron/adhesion traits to Bacteroides or Bifidobacterium.
Evidence
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PMID:34622230 - SUPPORT (COMPUTATIONAL)"Bifidobacterium persisters dedicated a significantly higher percentage of their genomes to CAZymes"
Bacteroides and Bifidobacterium First-Year Persistence
Bacteroides and Bifidobacterium were prominent among 59 of 560 early colonizer strains that persisted into late first-year sampling. The approximately 11 percent denominator is all eligible early strains, not each genus separately. Early detection was within the first two months; persistence required detection at month eight or later, accommodating missing or inadequate month-twelve samples. Strain matching used 99.999 percent population ANI over at least half the compared genome. This is observed persistence, not evidence that every member expressed adhesion or iron-acquisition traits.
Participating Taxa: persistent infant Bacteroides colonizers, persistent infant Bifidobacterium colonizers
Evidence
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PMID:34622230 - SUPPORT (IN_VIVO)"Approximately 11% of early colonizers, primarily Bacteroides and Bifidobacterium, persist during the first year of life"
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PMID:34622230 - SUPPORT (IN_VIVO)"When considering all infants, Bacteroides and Bifidobacterium strains were more likely to persist than were strains of other bacterial genera"
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which taxon-specific traits causally contribute to strain persistence?
The maternal-sharing and Bifidobacterium CAZyme routes remain partial models. E. coli iron-acquisition, adhesion and toxin annotations are positive genetic-potential results from three persisters versus 25 non-persisters, not expression, flux or knockout evidence. All three E. coli persisters came from preterm infants in a disease-enriched sample. #1515 tracks missing exact E. coli representation and valid trait structure; do not transfer those results to other taxa or erase them as negative evidence. Prematurity, early antibiotics, hospitalization and feeding covary, so the birth-status comparison is not an isolated cause. Full cached primary main text, Methods, Table 1 and figure captions read, but not external supplementary files, raw data, code or original images. One-community Edison dry run only; no paid report or new graph structure. Canonical taxonomy and non-graph fields are preserved, not recertified.
Attaches to: ecological_interactions#Maternal Strain Sharing and Persistence Association, ecological_interactions#Bifidobacterium Persister Carbohydrate-Gene Enrichment, ecological_interactions#Bacteroides and Bifidobacterium First-Year Persistence
External Resources
| Name | Repository | Resource ID |
|---|---|---|
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Primary publication for the infant gut strain persistence community
PubMed record for the Lou et al. 2021 Cell Rep Med paper. |
OTHER | PMID:34622230 |
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DOI landing page
DOI link to the Cell Rep Med paper. |
OTHER | doi:10.1016/j.xcrm.2021.100393 |
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| Birth status | full-term (n=13) vs preterm (n=9) infants | N/A |
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| Mother-infant pairing | 17 mother-infant pairs | N/A |
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