C. parapsilosis genomics in premature infant gut microbiome
18 fecal samples from neonates and infants at Magee-Womens Hospital, Pittsburgh, PA, analyzed for Candida parapsilosis genome diversity and in situ gene expression; case series design. machine-written summary
18 samples · 18 runs · US · Infant / toddler · 2021 · 12.89 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 54 sample values (age, collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 54 sample values (location locality, location region, location site) · PMC8215838 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 17 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 18 | 100% | ||||
| country | 18 | 100% | 18 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 18 | 100% | 18 | |||
| collection_date | 18 | 100% | 18 | |||
| detailed_location | 18 | 100% | ||||
| location_locality | 18 | 100% | 18 | |||
| location_region | 18 | 100% | 18 | |||
| location_site | 18 | 100% | 18 |
- Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics. PMID 34154658 PMC8215838 curated
Archive description
Candida parapsilosis is a common cause of invasive candidiasis, especially in newborn infants, and infections have been increasing over the past two decades. C. parapsilosis has been primarily studied in pure culture, leaving gaps in understanding of its function in a microbiome context. Here, we compare five unique C. parapsilosis genomes assembled from premature infant fecal samples, three of which are newly reconstructed, and analyze their genome structure, population diversity and in situ activity relative to reference strains in pure culture. All five genomes contain hotspots of single nucleotide variants, some of which are shared by strains from multiple hospitals. A subset of environmental and hospital-derived genomes share variants within these hotspots suggesting derivation of that region from a common ancestor. Four of the newly reconstructed C. parapsilosis genomes have four to sixteen copies of the gene RTA3, which encodes a lipid translocase and is implicated in antifungal resistance, potentially indicating adaptation to hospital antifungal use. Time course metatranscriptomics and metaproteomics on fecal samples from a premature infant with a C. parapsilosis blood infection revealed highly variable in situ expression patterns that are distinct from those of similar strains in pure cultures. For example, biofilm formation genes were relatively less expressed in situ, whereas genes linked to oxygen utilization were more highly expressed, indicative of growth in a relatively aerobic environment. In gut microbiome samples, C. parapsilosis coexisted with Enterococcus faecalis that shifted in relative abundance over time, accompanied by changes in bacterial and fungal gene expression and proteome composition. The results reveal potentially medically relevant differences in Candida function in gut vs. laboratory environments, and constrain evolutionary processes that could contribute to hospital strain persistence and transfer into premature infant microbiomes.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of infant / toddler and neonate by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.description · “from premature infant fecal samples, three of”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- body site study.description · “a C. parapsilosis blood infection revealed highly”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “microbiome of hospitalized infants revealed by in”
- life stage study.description · “candidiasis, especially in newborn infants, and infections”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN18948219 | age_at_collection_days | 12 | R1 | 0.90 | biosample_attr | 12 |
| SAMN18948219 | collection_date | 2017 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2017 |
| SAMN18948219 | country | US | R1 | 0.90 | biosample_attr | USA: Magee-Womens Hospital, Pittsburgh, PA |
| SAMN18948219 | location_locality | Pittsburgh | R3 | 0.70 | paper.fulltext.methods | Magee-Womens Hospital (Pittsburgh, PA) |
| SAMN18948219 | location_region | Pennsylvania | R3 | 0.70 | paper.fulltext.methods | Magee-Womens Hospital (Pittsburgh, PA) |
| SAMN18948219 | location_site | Magee-Womens Hospital | R3 | 0.70 | paper.fulltext.methods | housed in the Magee-Womens Hospital (Pittsburgh, PA) |
Sequencing
18 runs over 18 samples · mean 12.06 Gbp per run (median 12.89 Gbp, total 217.01 Gbp; 18 runs with a base count) · layout PAIRED 18 · platform ILLUMINA 18 · models Illumina NovaSeq 6000 (18) · 94% of runs with a Sandpiper profile · first public 2021-08-25
Authors (12)
West PT first · Peters SL · Olm MR · Yu FB · Gause H · Lou YC · Firek BA · Baker R · Johnson AD · Morowitz MJ · Hettich RL · Banfield JF last
Downloads
PRJNA717139.csv.gz (1.4 KB) · parquet (70.4 KB) — all 18 samples, every field with route and confidence · PRJNA717139_determinations.csv.gz (1.1 KB) — 108 evidence rows