A premature infant gut microbiome study that combines metagenomic and metatranscriptomic sequencing to probe the in situ physiological conditions experienced by Escherichia spp. in four premature infants (two of whom developed necrotizing enterocolitis, NEC). Twenty fecal samples spanning 4-6 time points per infant were analyzed using sample-specific metagenome-assembled genomes (MAGs) as references for transcript mapping, and a "diametric ratio" method that compares transcript ratios of genes with opposite transcription responses to eliminate biases related to organism abundance. Diametric ratios of genes associated with low oxygen levels were significantly higher in samples from infants later diagnosed with NEC than in samples without NEC, and the method extends to other physiological conditions such as nitric oxide exposure and osmotic pressure.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| premature-infant-gut Escherichia spp. — ontology label: Escherichia | NCBITaxon:561 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
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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.
Higher Low-Oxygen Diametric Ratios in NEC Samples
Escherichia transcript ratios associated with low oxygen were higher in samples from infants later diagnosed with NEC. This four-infant observational result suggests lower oxygen exposure, not directly measured hypoxia, microbial commensalism or proof of NEC causation. Twenty repeated samples are not twenty independent infants.
Participating Taxa: premature-infant-gut Escherichia spp.
Metabolites: oxygen (CHEBI:15379 · MediaIngredientMech · CMMMech)
Biological Processes:
- response to oxygen levels (GO:0070482 · PathwayMech)
Evidence
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PMID:32130257 - SUPPORT (IN_VIVO)"significantly higher diametric ratios of genes associated with low oxygen levels in samples of infants later diagnosed with NEC than in samples without NEC"
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Do transcript-ratio differences reflect NEC-related physiology or cohort confounding?
MAG mapping and diametric ratios are analytical methods, not ecological interactions. Full text reports lower NO-related ratios in NEC and an osmotic-ratio difference, but the latter significance wording conflicts with a printed p>0.05. Gestational age, delivery mode and birth weight differ between the two NEC and two control infants. Preserve those observations without diagnostic validation or causal arrows. Methods remain in the record description. Non-graph interpretation and source inconsistency remain #1722.
Attaches to: ecological_interactions#Higher Low-Oxygen Diametric Ratios in NEC Samples
2 evidence item(s)
significantly higher diametric ratios of genes associated with low oxygen levels in samples of infants later diagnosed with NEC than in samples without NEC
Supports the observed transcript-ratio association; physiological interpretation is indirect and confounded.
this method can be used for examining other physiological conditions, such as exposure to nitric oxide and osmotic pressure
Supports the method generalization.
External Resources
| Name | Repository | Resource ID |
|---|---|---|
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Primary publication for the premature-infant Escherichia community
PubMed record for the 2020 PLoS ONE paper. |
OTHER | PMID:32130257 |
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DOI landing page
DOI link to the PLoS ONE paper. |
OTHER | doi:10.1371/journal.pone.0229537 |
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| Cohort composition | 4 premature infants, 2 with NEC, 20 fecal samples | N/A |
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