Microbiome/virome in healthy Danish adults on antibiotics
59 samples from healthy adult controls in Denmark, studying gut microbiome and virome changes during antibiotic treatment, using an intervention design. machine-written summary
59 samples · 59 runs · DK · Age unknown · 2019 · 11.36 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 59 sample values (country) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 177 sample values (antibiotic exposure, health condition, health condition detail) · PMC10536327, PMC7778953, PMC8018486 |
| ○ 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 |
intervention — arms not resolved
Antibiotic given as the study intervention (incl. eradication therapy design single_arm_before_after · population healthy_control · Broad-spectrum antibiotic administration to healthy adults, gut microbiome sampled over time
“comprehensively assess the effects of antibiotics on the gut microbiota” — abstract:33779498 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
Schedule stated by the source: “stool samples over a 4-month period, before, during, and after antibiotic exposure” (time origin: intervention_start); stated follow-up 4 mo.
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 | 59 | 100% | ||||
| country | 59 | 100% | 59 | |||
| health_condition | 59 | 100% | 59 | |||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 59 | 100% | 59 | |||
| health_condition_detail | 59 | 100% | 59 |
- Expansion and persistence of antibiotic-specific resistance genes following antibiotic treatment. 2021 PMID 33779498 PMC8018486 own_data
- mMGE: a database for human metagenomic extrachromosomal mobile genetic elements. 2021 PMID 33074335 PMC7778953 unsure
- Uncovering Predictive Factors and Interventions for Restoring Microecological Diversity after Antibiotic Disturbance. 2023 PMID 37764709 PMC10536327 unsure
Archive description
Human gut microbiome and virome under antibiotic treatment
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host study.title · “Human gut microbiome and virome”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SRR10423891 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | not received antibiotic treatment 1 year prior |
| SRR10423891 | country | DK | R1 | 0.60 | biosample.attribute:geo_loc_name | geo_loc_name: Denmark |
| SRR10423891 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | Ten healthy adult volunteers |
| SRR10423891 | health_condition_detail | healthy adult volunteers / healthy individuals | R3 | 0.70 | paper.fulltext.methods | Ten healthy adult volunteers |
Sequencing
59 runs over 59 samples · mean 11.65 Gbp per run (median 11.36 Gbp, total 687.07 Gbp; 59 runs with a base count) · layout PAIRED 59 · platform ILLUMINA 59 · models Illumina HiSeq 2000 (59) · 93% of runs with a Sandpiper profile · first public 2019-11-11
Authors (31)
Lai S first · Jia L · Subramanian B · Pan S · Zhang J · Dong Y · Chen WH · Zhao XM last · Kang K first · Imamovic L · Misiakou MA · Bornakke Sørensen M · Heshiki Y · Ni Y · Zheng T · Li J · Ellabaan MMH · Colomer-Lluch M · Rode AA · Bytzer P · Panagiotou G · Sommer MOA last · Chen J first · Zhu J · Lu W · Wang H · Pan M · Tian P · Zhao J · Zhang H · Chen W last
Downloads
PRJNA588313.csv.gz (2.1 KB) · parquet (70.5 KB) — all 59 samples, every field with route and confidence · PRJNA588313_determinations.csv.gz (1.6 KB) — 236 evidence rows