An in situ infant gut microbiome study of Candida parapsilosis colonization in hospitalized infants, combining metagenomics, metatranscriptomics, and metaproteomics. Infant-06 fecal samples recovered C. parapsilosis alongside Enterococcus faecalis, Lactobacillus gasseri, and Staphylococcus epidermidis; the time series placed Candida in an early low-complexity gut community, followed its replacement or outnumbering largely by E. faecalis, and linked Candida-positive samples to shifts in Enterococcus ribosomal and mannitol phosphotransferase-system transcript features.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Candida parapsilosis — ontology label: Lodderomyces parapsilosis | NCBITaxon:5480 · TaxonMech · TraitMech | N/A | |
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| Enterococcus faecalis | NCBITaxon:1351 · 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.
Repeated Candida-Enterococcus Co-Detection
E. faecalis was detected in seven Candida-positive infants. These include Candida species, not seven independently established C. parapsilosis-specific interactions. Co-detection alone is not colonization facilitation.
Biological Processes:
- biological process involved in interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
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PMID:34154658 - SUPPORT (IN_VIVO)"in every infant where a Candida genome was assembled or detected through read mapping, E. faecalis was also present"
Relative Candida-Enterococcus Succession
In infant 06, early C. parapsilosis relative dominance gave way to E. faecalis predominance. This compositional change does not establish competition, absolute fungal decline or eradication; fungal transcripts and peptides remained detectable.
Biological Processes:
- biological process involved in interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
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PMID:34154658 - SUPPORT (IN_VIVO)"C. parapsilosis is highly abundant relative to other organisms in the first 20 days of life"
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PMID:34154658 - SUPPORT (IN_VIVO)"before quickly being replaced or outnumbered, largely by E. faecalis"
Candida-Positive Enterococcus Mannitol-PTS Response
CROSS_FEEDINGHYPOTHESIZED - mannitol-associated E. faecalis transcription could reflect Candida-derived substrate use. Mannitol production was reported for another fungal strain, not traced from infant strain C1_006. Between-infant differences confound attribution, and ribosomal transcripts do not directly measure growth rate.
Source Taxon: Candida parapsilosis
Target Taxon: Enterococcus faecalis
Metabolites: D-mannitol (CHEBI:16899 · MediaIngredientMech · CMMMech)
Biological Processes:
- carbohydrate transport (GO:0008643 · PathwayMech)
Evidence
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PMID:34154658 - PARTIAL (IN_VIVO)"ribosomal proteins all showed higher expression in situ, suggesting increased E. faecalis growth rate in the presence of C. parapsilosis"
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PMID:34154658 - PARTIAL (IN_VIVO)"mannitol-specific phosphotransferase system (PTS) transporters upregulated in Candida-positive samples"
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PMID:34154658 - PARTIAL (IN_VIVO)"Mannitol-1-phosphate 5-dehydrogenase, an enzyme responsible for the conversion of D-mannitol to fructose"
In Situ Candida Biofilm- and Respiration-Associated Transcripts
Infant-strain transcripts differed from heterogeneous pure-culture comparisons in biofilm-associated and respiration-related annotations. These changes do not measure biofilm mass, oxygen tension, respiration flux, niche partitioning or virulence; ortholog annotations are not exact-system functional validation.
Participating Taxa: Candida parapsilosis
Evidence
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PMID:34154658 - SUPPORT (IN_VIVO)"Biofilm formation showed lower expression overall in situ"
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PMID:34154658 - SUPPORT (IN_VIVO)"Up in situ was enriched for KEGG families for LSM"
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PMID:34154658 - SUPPORT (IN_VIVO)"Cytochrome c oxidase and bc1 complex"
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Does strain-resolved mannitol transfer explain the transcriptional association after controlling for infant differences?
PMID:34154658 proposes exchange but does not trace it. The strongest in-situ fungal characterization is one strain in one infant; treatment and host differences remain confounders. Genome reconstruction is analysis workflow, so its node is removed. The four previously pruned arrows remain absent.
Attaches to: ecological_interactions#Repeated Candida-Enterococcus Co-Detection, ecological_interactions#Relative Candida-Enterococcus Succession, ecological_interactions#Candida-Positive Enterococcus Mannitol-PTS Response, ecological_interactions#In Situ Candida Biofilm- and Respiration-Associated Transcripts
External Resources
| Name | Repository | Resource ID |
|---|---|---|
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Primary publication for the C. parapsilosis hospitalized-infant community
PubMed record for the West et al. 2021 Microbiome paper. |
OTHER | PMID:34154658 |
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DOI landing page
DOI link to the Microbiome paper. |
OTHER | doi:10.1186/s40168-021-01085-y |
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| Clinical setting | hospitalized infants | N/A |
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