Gut virome changes after H. pylori eradication therapy
1 fecal sample from an adult with a GI infection, part of a longitudinal study tracking gut virome and microbiota changes in H. pylori-infected patients before and after antibiotic eradication therapy. machine-written summary
121 samples · 121 runs · HK · Age unknown · 2022 · 8.00 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 363 sample values (intervention, subject id, timepoint) |
| ✓ Abstract / description | 121 sample values (antibiotic exposure) |
| ✓ Full text | 363 sample values (country, health condition, health condition detail) · PMC10110541 |
| ✓ Supplementary tables | 121 sample values (sex) |
| – 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 resolved
44 people have samples in more than one arm.
Antibiotic given as the study intervention (incl. eradication therapy design single_arm_before_after · population gi_infection_or_diarrhoea · H. pylori eradication antibiotic therapy, sampled before/after
“antibiotics therapy for Helicobacter pylori” — abstract:37069161 (study level; per-sample arms are in the intervention column below)
longitudinal
44 of 44 people sampled more than once (121 samples; median 3, up to 3 per person) · follow-up median 6 mo (max 6 mo) · median interval between samples 42 d (time from timepoint labels). Schedule stated by the source: “stool at baseline, 6-week and 6-month after treatment” (time origin: treatment_start).
Each row is one person (36 shown of 44); dots are samples at days since that person's first sample.
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 | 121 | 100% | ||||
| country | 121 | 100% | 121 | |||
| health_condition | 121 | 100% | 121 | |||
| subject_id | 121 | 100% | 121 | |||
| antibiotic_exposure | 121 | 100% | 121 | |||
| health_condition_detail | 121 | 100% | 121 | |||
| intervention | 121 | 100% | 121 | |||
| sex | 121 | 100% | 121 | |||
| timepoint_label | 121 | 100% | 121 |
- Altered human gut virome in patients undergoing antibiotics therapy for Helicobacter pylori. 2023 PMID 37069161 PMC10110541 own_data
Archive description
Human fecal sample DNA-seq reads
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.57. Assay shotgun_dna.
- host study.title · “Homo sapiens Raw sequence reads”
- body site study.description · “Human fecal sample DNA-seq reads”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SRR15236584 | antibiotic_exposure | yes | R4 | 0.50 | paper.abstract | undergoing antibiotics therapy for Helicobacter pylori |
| SRR15236584 | country | HK | R3 | 0.70 | paper.fulltext.methods | Hospital Authority Hong Kong West Cluster |
| SRR15236584 | health_condition | gi_infection_or_diarrhoea | R3 | 0.70 | paper.fulltext.methods | 44 adult patients with confirmed H. pylori infection |
| SRR15236584 | health_condition_detail | confirmed H. pylori infection | R3 | 0.70 | paper.fulltext.methods | 44 adult patients with confirmed H. pylori infection |
| SRR15236584 | intervention | antibiotic | R1 | 0.70 | sample.name_rule:library_name | library_name: ARG037-02ST-01-DNA |
| SRR15236584 | sex | male | R2 | 0.75 | paper.supp.41467_2023_37975_MOESM3_ESM.xlsx[Supplementary Data 1!Sex] | ARG#: ARG037; Sex: Male |
| SRR15236584 | subject_id | ARG037 | R1 | 0.70 | sample.name_rule:library_name | library_name: ARG037-02ST-01-DNA |
| SRR15236584 | timepoint_label | 6-month | R1 | 0.70 | sample.name_rule:library_name | library_name: ARG037-02ST-01-DNA |
Sequencing
121 runs over 121 samples · mean 8.16 Gbp per run (median 8.00 Gbp, total 987.69 Gbp; 121 runs with a base count) · layout PAIRED 121 · platform ILLUMINA 121 · models Illumina NovaSeq 6000 (121) · 93% of runs with a Sandpiper profile · first public 2022-02-17
Downloads
PRJNA749138.csv.gz (3.6 KB) · parquet (73.9 KB) — all 121 samples, every field with route and confidence · PRJNA749138_determinations.csv.gz (8.2 KB) — 968 evidence rows