Gut metagenomes, H. pylori eradication therapy, Russia
15 fecal metagenome samples from patients with H. pylori infection in Russia, collected longitudinally before, immediately after, and several weeks after antibiotic eradication therapy to profile gut microbiota changes. machine-written summary
15 samples · 15 runs · RU · Age unknown · 2017 · 1.70 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 60 sample values (collection date, country, latitude, longitude) |
| ✓ Abstract / description | 15 sample values (antibiotic exposure) |
| ✓ Full text | 75 sample values (health condition, health condition detail, location locality, location site, sex) · PMC5554923 |
| ✓ Supplementary tables | 30 sample values (subject id, timepoint) |
| – 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 gi_infection_or_diarrhoea · H. pylori eradication therapy with two broad-spectrum antibiotics, sampled before/after
“before the start of the eradication, immediately after eradication” — abstract:28831408 (study level; per-sample arms are in the intervention column below)
longitudinal
5 of 5 people sampled more than once (15 samples; median 3, up to 3 per person) · follow-up median 42 d (max 3 mo) · median interval between samples 16 d (time from visit codes mapped to the stated schedule). Schedule stated by the source: “3 time points per patient: before start of eradication therapy, immediately after therapy, and several weeks after end of treatment” (time origin: intervention_start).
Each row is one person (5 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 | 0 | 0% | ||||
| country | 15 | 100% | 15 | |||
| health_condition | 15 | 100% | 15 | |||
| subject_id | 15 | 100% | 15 | |||
| antibiotic_exposure | 15 | 100% | 15 | |||
| collection_date | 15 | 100% | 15 | |||
| detailed_location | 15 | 100% | ||||
| health_condition_detail | 15 | 100% | 15 | |||
| latitude | 15 | 100% | 15 | |||
| location_locality | 15 | 100% | 15 | |||
| location_site | 15 | 100% | 15 | |||
| longitude | 15 | 100% | 15 | |||
| sex | 15 | 100% | 15 | |||
| timepoint_label | 15 | 100% | 15 |
- Shotgun metagenomic data on the human stool samples to characterize shifts of the gut microbial profile after the Helicobacter pylori eradication therapy. 2017 PMID 28831408 PMC5554923 own_data
Archive description
Helicobacter pylori was reported to be one of the most common reasons of gastric diseases. According to the Maastricht V Consensus, patients with H. pylori infection are prescribed a two-week eradication therapy consisted of 2 types of broad spectrum antibiotics. Such treatment can negatively affect the gut microbiota of patients by decreasing the number of members of the normal bacterial flora. The metagenomic analisys of the fecal microbiota of patients with H. pylori infection at 3 time points (before the start of the eradication therapy, immediately after the therapy and several weeks after the end of treatment) could help to reveal the taxonomic and functional changes in intestinal microflora and to detect molecular markers of gastrointestinal diseases pathogenesis.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.title · “fecal microbiota of patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA104128061 | antibiotic_exposure | yes | R4 | 0.40 | study.description | two-week eradication therapy consisted of 2 types of broad spectrum antibiotics |
| SAMEA104128061 | collection_date | 2014 | R1 | 0.90 | biosample.attribute:collection_date | 2014 |
| SAMEA104128061 | country | RU | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Russia |
| SAMEA104128061 | health_condition | gi_infection_or_diarrhoea | R3 | 0.70 | paper.fulltext.methods | Helicobacter pylori detected by endoscopy were taken for analysis |
| SAMEA104128061 | health_condition_detail | H. pylori infection with stomach/duodenum disease symptoms | R3 | 0.70 | paper.fulltext.methods | Helicobacter pylori detected by endoscopy were taken for analysis |
| SAMEA104128061 | latitude | 55.0000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 55 49 |
| SAMEA104128061 | location_locality | Kazan | R3 | 0.70 | paper.fulltext.methods | Polyclinic Department of the Republican Clinical Hospital #2 (Kazan) |
| SAMEA104128061 | location_site | Polyclinic Department of the Republican Clinical Hospital #2 | R3 | 0.70 | paper.fulltext.methods | Republican Clinical Hospital #2 (Kazan) |
| SAMEA104128061 | longitude | 49.0000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 55 49 |
| SAMEA104128061 | sex | male | R3 | 0.85 | paper.body.Table 1[Gender] | Male |
| SAMEA104128061 | subject_id | 1 | R2 | 0.85 | paper.body.Table 1[Patient ID] | 1HP: patient 1 |
| SAMEA104128061 | timepoint_label | time point 1 | R2 | 0.85 | paper.body.Table 1[Time point] | 1HP: time point 1 |
Sequencing
15 runs over 15 samples · mean 1.52 Gbp per run (median 1.70 Gbp, total 22.81 Gbp; 15 runs with a base count) · layout SINGLE 15 · platform ABI_SOLID 15 · models AB 5500xl-W Genetic Analysis System (15) · 0% of runs with a Sandpiper profile · first public 2017-06-22
Authors (9)
Boulygina EA first · Markelova MI · Khusnutdinova DR · Siniagina MN · Malanin SY · Abdulkhakov RA · Abdulkhakov SR · Chernov VM · Grigoryeva TV last
Downloads
PRJEB21338.csv.gz (1.5 KB) · parquet (72.0 KB) — all 15 samples, every field with route and confidence · PRJEB21338_determinations.csv.gz (2.2 KB) — 180 evidence rows