Oligosaccharide, probiotic effects post-antibiotic
316 samples from healthy adult and elderly volunteers in the USA, studying antibiotic treatment combined with a prebiotic/fibre and probiotic intervention on the gut microbiome. machine-written summary
316 samples · 316 runs · US · Adult · 2023 · 2.27 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,580 sample values (age, country, sex, subject id, timepoint) |
| ✓ Abstract / description | 948 sample values (antibiotic exposure, 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
Antibiotic given as the study intervention (incl. eradication therapy Prebiotic / dietary fibre supplement Probiotic (live microorganisms; single strain or mixture) design randomized_controlled_trial · population healthy_control · Complex oligosaccharide with/without probiotic in antibiotic-treated healthy volunteers
“complex oligosaccharide with and without a probiotic” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
53 of 53 people sampled more than once (316 samples; median 6, up to 6 per person) · follow-up median 34 d (max 34 d) · median interval between samples 5 d (time from timepoint numbers, unit from the stated sampling schedule). Schedule stated by the source: “53 subjects sampled repeatedly (median/max 6/6 samples each) at study days 1, 5, 9, 14, 28, 35” (time origin: other); stated follow-up 35 d.
Each row is one person (36 shown of 53); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 284 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 | 316 | 100% | ||||
| country | 316 | 100% | 316 | |||
| health_condition | 316 | 100% | 316 | |||
| subject_id | 316 | 100% | 316 | |||
| age_at_collection_days | 316 | 100% | 316 | |||
| antibiotic_exposure | 316 | 100% | 316 | |||
| health_condition_detail | 316 | 100% | 316 | |||
| sex | 316 | 100% | 316 | |||
| timepoint_label | 316 | 100% | 316 |
- Precision modulation of dysbiotic adult microbiomes with a human-milk-derived synbiotic reshapes gut microbial composition and metabolites. 2023 PMID 37657443 own_data
Archive description
The study evaluates the synergy of the use of a complex oligosaccharide with and without a probiotic on the human microbiome in antibiotic-treated healthy volunteers.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by opus_adjudicated with confidence 0.60. Assay shotgun_dna.
- host study.title · “antibiotic-treated human microbiome”
- host run.scientific_name · “Homo sapiens”
- body site sample.attr.tissue · “stool (n=316/316)”
- life stage sample.attr.age · “31 (n=250/316)”
- life stage sample.attr.age · “67 (n=66/316)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN36676629 | age_at_collection_days | 12783.8 | R1 | 0.85 | sample.attr.age | 35 |
| SAMN36676629 | antibiotic_exposure | yes | R4 | 0.50 | study.description | antibiotic-treated healthy volunteers |
| SAMN36676629 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN36676629 | health_condition | healthy_control | R4 | 0.50 | paper.abstract | we induced dysbiosis in 56 healthy volunteers using antibiotics to test a synbiotic |
| SAMN36676629 | health_condition_detail | healthy volunteers | R4 | 0.50 | paper.abstract | induced dysbiosis in 56 healthy volunteers using antibiotics |
| SAMN36676629 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN36676629 | subject_id | NS001 | R1 | 0.70 | sample.name_rule:alias | NS001D101 |
| SAMN36676629 | timepoint_label | 1 | R1 | 0.85 | sample.attr.day_of_study | 1 |
Sequencing
316 runs over 316 samples · mean 2.24 Gbp per run (median 2.27 Gbp, total 707.10 Gbp; 316 runs with a base count) · layout PAIRED 316 · platform ILLUMINA 316 · models Illumina NovaSeq 6000 (316) · 90% of runs with a Sandpiper profile · first public 2023-09-02
Authors (0)
No author record.
Downloads
PRJNA993161.csv.gz (8.8 KB) · parquet (81.1 KB) — all 316 samples, every field with route and confidence · PRJNA993161_determinations.csv.gz (13.7 KB) — 2,528 evidence rows