Gut colonization in a premature infant (case series)
1 stool sample from a premature infant (born at 28 weeks gestation), analyzed by metagenomic and 16S rRNA sequencing to track microbial gut colonization over time; case series design. machine-written summary
1 samples · 18 runs · US · Infant / toddler · 2012 · 27.44 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ✓ Abstract / description | 1 sample values (subject id) |
| ✓ Full text | 4 sample values (antibiotic exposure, country, location locality, preterm status) · PMC6905865, PMC8296540 |
| ○ 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 1 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 | 1 | 100% | ||||
| country | 1 | 100% | 1 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 1 | 100% | 1 | |||
| antibiotic_exposure | 1 | 100% | 1 | |||
| detailed_location | 1 | 100% | ||||
| location_locality | 1 | 100% | 1 | |||
| preterm_status | 1 | 100% | 1 |
- Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria. PMID 31844663 PMC6905865 curated
- METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs. PMID 34294039 PMC8296540 curated
Archive description
Stool sample from a premature human infant (UC1). <p> This study used metagenomic methods (community genomic analysis and sequencing of amplified 16S rRNA genes) to document microbial colonization of the gut of a premature infant born at 28 weeks gestation. Analysis of 16S rRNA gene sequences collected approximately daily revealed three compositional phases during colonization. We reconstructed genomes of the dominant organisms and intensively curated population genomic datasets from the third phase. In the third phase, the communities were dominated by a nearly clonal Serratia population, two Citrobacter strains sharing >99% nucleotide identity, and contained a lower abundance Enterococcus population, multiple plasmids and bacteriophage. The relative abundance of the Citrobacter strains changed significantly over time. Modeling of Citrobacter strain abundances suggests differences in growth rates and/or host colonization patterns. We identified genotypic variation potentially responsible for divergent strain ecologies, including hotspots of sequence variation in regulatory genes and intergenic regions, and in genes involved in transport, flagellar biosynthesis, substrate metabolism, and host colonization, as well as differences in the complements of these genes. Our results demonstrate that a community genomic approach can elucidate gut microbial colonization at the resolution required to discern medically relevant strain and species population dynamics, and hence improve our ability to diagnose and treat microbial community-mediated disorders.
How this project entered the registry
Classified as human gut / stool 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.title · “analysis of infant stool sample”
- body site study.description · “Stool sample from a”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Metagenomic analysis of infant stool sample”
- life stage study.description · “sample from a premature human infant (UC1).”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN00990124 | antibiotic_exposure | yes | R3 | 0.40 | paper.fulltext.results | prophylactic antibiotics given to all premature infants at birth |
| SAMN00990124 | country | US | R3 | 0.40 | paper.fulltext.results | recruited from the University of Pittsburgh Medical Center |
| SAMN00990124 | location_locality | Pittsburgh, PA | R3 | 0.60 | paper.fulltext.results | Magee-Womens Hospital (Pittsburgh, PA) over a 5-year period |
| SAMN00990124 | preterm_status | preterm | R3 | 0.50 | paper.fulltext.abstract | 1163 fecal samples from premature infants |
| SAMN00990124 | subject_id | PRJNA60717 | R4 | 0.65 | design.single_subject:description | Stool sample from a premature human infant (UC1). |
Sequencing
18 runs over 1 samples · mean 1.52 Gbp per run (median 1.26 Gbp, total 27.44 Gbp; 18 runs with a base count) · layout PAIRED 18 · platform ILLUMINA 18 · models Illumina HiSeq 2000 (18) · 100% of runs with a Sandpiper profile · first public 2012-09-12
Authors (15)
Morowitz MJ first · Denef VJ · Costello EK · Thomas BC · Poroyko V · Relman DA · Banfield JF last · Olm MR first · Bhattacharya N · Crits-Christoph A · Firek BA · Baker R · Song YS · Zhang Z first · Zhang L last
Downloads
PRJNA60717.csv.gz (878 B) · parquet (69.1 KB) — all 1 samples, every field with route and confidence · PRJNA60717_determinations.csv.gz (969 B) — 5 evidence rows