Pediatric gut microbiome recovery after Salmonella infection
13 longitudinal fecal samples from hospitalized pediatric patients with Salmonella gastrointestinal infection, tracking gut microbiome recovery during probiotic-associated treatment. machine-written summary
13 samples · 13 runs · CN · Child · 2026 · 12.03 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 91 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 26 sample values (health condition, health condition detail) |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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
Probiotic (live microorganisms; single strain or mixture) design single_arm_before_after · population gi_infection_or_diarrhoea · Probiotic-associated intervention during recovery
“probiotic-associated intervention” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
2 of 2 people sampled more than once (13 samples; median 6, up to 7 per person) · follow-up median 4 mo (max 5 mo) · median interval between samples 12 d (time from collection dates). Schedule stated by the source: “Serial fecal samples per patient across acute infection, antimicrobial treatment, recovery, and follow-up (8 distinct timepoint labels, 13 samples total from 2 subjects).”.
Each row is one person (2 shown); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 13 | 100% | ||||
| country | 13 | 100% | 13 | |||
| health_condition | 13 | 100% | 13 | |||
| subject_id | 13 | 100% | 13 | |||
| collection_date | 13 | 100% | 13 | |||
| detailed_location | 13 | 100% | ||||
| health_condition_detail | 13 | 100% | 13 | |||
| latitude | 13 | 100% | 13 | |||
| location_region | 13 | 100% | 13 | |||
| longitude | 13 | 100% | 13 | |||
| timepoint_label | 13 | 100% | 13 |
Archive description
This study examines the genomic characteristics, antimicrobial resistance, and longitudinal gut microbiome dynamics associated with pediatric Salmonella infection. Bacterial isolates and serial fecal samples were collected from two hospitalized pediatric patients during acute infection, antimicrobial treatment, recovery, and follow-up. Whole-genome sequencing of bacterial isolates was integrated with shotgun metagenomic sequencing, plasmid reconstruction, antimicrobial susceptibility testing, and conjugation assays to investigate carbapenem-resistant Enterobacteriaceae, antimicrobial resistance determinants, plasmid-mediated resistance, and their dynamics within the intestinal ecosystem. The study also evaluates longitudinal changes in the gut microbial community during clinical recovery and probiotic-associated intervention.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host study.description · “serial fecal samples were collected from two hospitalized pediatric patients”
- body site study.description · “longitudinal gut microbiome dynamics”
- life stage study.title · “pediatric Salmonella infection”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN62531683 | collection_date | 2024-08-18 | R1 | 0.90 | biosample.attribute:collection_date | 2024-08-18 |
| SAMN62531683 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China: Zhejiang |
| SAMN62531683 | health_condition | gi_infection_or_diarrhoea | R4 | 0.30 | study.description | pediatric Salmonella infection |
| SAMN62531683 | health_condition_detail | Salmonella infection | R4 | 0.50 | study.description | pediatric Salmonella infection |
| SAMN62531683 | latitude | 30.2741 | R1 | 0.90 | biosample.attribute:lat_lon | 30.2741 N 120.1551 E |
| SAMN62531683 | location_region | Zhejiang | R1 | 0.85 | biosample.attribute:geo_loc_name | China: Zhejiang |
| SAMN62531683 | longitude | 120.1551 | R1 | 0.90 | biosample.attribute:lat_lon | 30.2741 N 120.1551 E |
| SAMN62531683 | subject_id | S | R1 | 0.70 | sample.name_rule:library_names | S1_lib |
| SAMN62531683 | timepoint_label | 1 | R1 | 0.70 | sample.name_rule:library_names | S1_lib |
Sequencing
13 runs over 13 samples · mean 12.35 Gbp per run (median 12.03 Gbp, total 160.54 Gbp; 13 runs with a base count) · layout PAIRED 12, SINGLE 1 · platform ILLUMINA 13 · models Illumina NovaSeq 6000 (13) · 0% of runs with a Sandpiper profile · first public 2026-08-23
Authors (0)
No author record.
Downloads
PRJNA1514298.csv.gz (1.3 KB) · parquet (70.7 KB) — all 13 samples, every field with route and confidence · PRJNA1514298_determinations.csv.gz (1.5 KB) — 117 evidence rows