Gut microbiome in paediatric short bowel syndrome, St. Louis
Longitudinal cohort of 67 shotgun metagenomic samples from children with short bowel syndrome in St. Louis, USA, examining antibiotic-driven intestinal dysbiosis and its association with gut-derived bloodstream infections. machine-written summary
67 samples · 67 runs · US · Infant / toddler · 2021 · 1.27 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 77 sample values (country, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC8284144 |
| ✓ Supplementary tables | 283 sample values (age, antibiotic exposure, gestational age weeks, sex, subject id) |
| – 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 |
intervention — arms not resolved
design observational_with_procedure · Surgical intestinal resection resulting in short bowel syndrome
longitudinal
13 of 23 people sampled more than once (57 samples; median 4, up to 8 per person) · follow-up median 21 mo (max 2.8 y) · median interval between samples 5 mo (time from age at collection). Schedule stated by the source: “Serial stool collection over the first four years of life per SBS patient; one participant also sampled later in adolescence.” (time origin: birth).
Each row is one person (11 shown of 13); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 62 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 | 57 | 85% | ||||
| country | 67 | 100% | 67 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 67 | 100% | 10 | 57 | ||
| age_at_collection_days | 57 | 85% | 57 | |||
| gestational_age_weeks | 57 | 85% | 57 | |||
| sex | 57 | 85% | 57 | |||
| antibiotic_exposure | 55 | 82% | 55 |
- Antibiotic-driven intestinal dysbiosis in pediatric short bowel syndrome is associated with persistently altered microbiome functions and gut-derived bloodstream infections. PMID 34264786 PMC8284144 curated
Archive description
Shotgun metagenomic sequencing of the intestinal microbiota of children with short bowel syndrome and genome sequencing of blood stream infection isolates Raw sequence reads
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of child and infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “Antibiotic-driven intestinal dysbiosis in paediatric”
- body site study.description · “sequencing of the intestinal microbiota of children”
- body site study.title · “associated with gut-derived blood stream infections throughout”
- body site study.description · “genome sequencing of blood stream infection isolates”
- life stage study.title · “intestinal dysbiosis in paediatric SBS alters microbiome”
- life stage study.description · “intestinal microbiota of children with short bowel”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN18016864 | age_at_collection_days | 266 | R2 | 0.85 | paper.supp.table | Day_of_life=266 |
| SAMN18016864 | antibiotic_exposure | yes | R2 | 0.85 | paper.supp.KGMI_A_1940792_SM0926.zip/Supplementary information/Supplementary Data Table 1.xlsx[210105_case_metadata][Antibiotics_current] | Yes |
| SAMN18016864 | country | US | R1 | 0.90 | biosample_attr | USA: St. Louis |
| SAMN18016864 | gestational_age_weeks | 29.6 | R2 | 0.85 | paper.supp.table | GA_birth=29.6 |
| SAMN18016864 | sex | female | R2 | 0.85 | paper.supp.table | Gender=F |
| SAMN18016874 | subject_id | 05 | R1 | 0.70 | biosample.attribute:sample_identifier | SGS_05_001 |
| SAMN18016864 | subject_id | SGS_01 | R2 | 0.85 | paper.supp.KGMI_A_1940792_SM0926.zip/Supplementary information/Supplementary Data Table 1.xlsx[210105_case_metadata][Patient_ID] | SGS_01 |
Sequencing
67 runs over 67 samples · mean 1.24 Gbp per run (median 1.27 Gbp, total 83.25 Gbp; 67 runs with a base count) · layout PAIRED 67 · platform ILLUMINA 67 · models NextSeq 500 (67) · 93% of runs with a Sandpiper profile · first public 2021-07-28
Authors (17)
Thänert R first · Thänert A · Ou J · Bajinting A · Burnham CD · Engelstad HJ · Tecos ME · Ndao IM · Hall-Moore C · Rouggly-Nickless C · Carl MA · Rubin DC · Davidson NO · Tarr PI · Warner BB · Dantas G · Warner BW last
Downloads
PRJNA701982.csv.gz (3.1 KB) · parquet (73.3 KB) — all 67 samples, every field with route and confidence · PRJNA701982_determinations.csv.gz (3.9 KB) — 360 evidence rows