Microbiota shifts after H. pylori eradication, Kazan, Russia
92 gut metagenome samples from adult and elderly patients in Kazan, Russia, with H. pylori infection, studied before and after eradication therapy (amoxicillin, clarithromycin, and adjuncts) in an intervention design. machine-written summary
92 samples · 92 runs · RU · Adult · 2017 · 1.42 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 920 sample values (age, collection date, country, latitude, location locality, location region, longitude, sex) |
| ✓ Abstract / description | 92 sample values (antibiotic exposure) |
| ○ Full text | read; no usable statement or table · PMC6718723 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 184 sample values (health condition, health condition detail) · from GMrepo v3 |
| – 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 Non-antibiotic pharmaceutical given as the study intervention (metformin design single_arm_before_after · population gi_infection_or_diarrhoea · Quadruple HP eradication: amoxicillin, clarithromycin, PPI, bismuth subsalicylate
“peroral administration amoxicillin and clarithromycin and others additional substances” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
Schedule stated by the source: “Same patients sampled at up to 3 timepoints (before and after H. pylori eradication therapy); point_number/timepoint_label = 1,2,3.” (time origin: treatment start).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 92 | 100% | ||||
| country | 92 | 100% | 92 | |||
| health_condition | 92 | 100% | 92 | |||
| subject_id | 92 | 100% | 92 | |||
| age_at_collection_days | 92 | 100% | 92 | |||
| antibiotic_exposure | 92 | 100% | 92 | |||
| collection_date | 92 | 100% | 92 | |||
| detailed_location | 92 | 100% | ||||
| health_condition_detail | 92 | 100% | 92 | |||
| latitude | 92 | 100% | 92 | |||
| location_locality | 92 | 100% | 92 | |||
| location_region | 92 | 100% | 92 | |||
| longitude | 92 | 100% | 92 | |||
| sex | 92 | 100% | 92 | |||
| timepoint_label | 92 | 100% | 92 |
- Shifts in the Human Gut Microbiota Structure Caused by Quadruple Helicobacter pylori Eradication Therapy. 2019 PMID 31507546 PMC6718723 unsure
Archive description
Here presented gut metagenomic samples from patients with Helicobacter pylori before and after eradication therapy. The data was obtained by ABI/SOLID platform in colorspase format. The therapy included peroral administration amoxicillin and clarithromycin and others additional substances (such as proton pump inhibitor and subsalicylate of bismuth). This data was used for determine shifts of taxonomic and functional profile caused by treatment. The study were financially supported by the Russian Scientific Foundation (grant # 15-14-00066).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by opus_adjudicated with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “patients with Helicobacter pylori”
- body site study.description · “gut metagenomic samples from patients”
- body site study.title · “Shifts of the intestinal microbiota and resistome”
- life stage sample.attr.host_age · “31 (n=79/92)”
- life stage sample.attr.host_age · “69 (n=11/92)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07759909 | age_at_collection_days | 11312.8 | R1 | 0.85 | sample.attr.host_age | 31 |
| SAMN07759909 | antibiotic_exposure | yes | R4 | 0.50 | study.description | peroral administration amoxicillin and clarithromycin |
| SAMN07759909 | collection_date | 2016 | R1 | 0.90 | biosample.attribute:collection_date | 2016 |
| SAMN07759909 | country | RU | R1 | 0.90 | sample.attr.geo_loc_name | Russia: Kazan |
| SAMN07759909 | health_condition | gi_infection_or_diarrhoea | R2 | 0.75 | external.gmrepo source | phenotype: Helicobacter Infections |
| SAMN07759909 | health_condition_detail | Helicobacter Infections | R2 | 0.75 | external.gmrepo source | phenotype: Helicobacter Infections |
| SAMN07759909 | latitude | 55.7908 | R1 | 0.90 | biosample.attribute:lat_lon | 55.790833 N 49.114444 E |
| SAMN07759909 | location_locality | Kazan | R1 | 0.85 | biosample.attribute:geo_loc_name | Russia: Kazan |
| SAMN07759909 | location_region | Tatarstan | R1 | 0.60 | biosample.attribute:lat_lon | 55.790833 N 49.114444 E |
| SAMN07759909 | longitude | 49.1144 | R1 | 0.90 | biosample.attribute:lat_lon | 55.790833 N 49.114444 E |
| SAMN07759909 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN07759909 | subject_id | 5HP | R1 | 0.85 | sample.attr.unique_id | 5HP |
| SAMN07759909 | timepoint_label | 1 | R1 | 0.85 | biosample.attribute:point_number | 1 |
Sequencing
92 runs over 92 samples · mean 1.48 Gbp per run (median 1.42 Gbp, total 135.75 Gbp; 92 runs with a base count) · layout SINGLE 92 · platform ABI_SOLID 92 · models AB 5500 Genetic Analyzer (92) · 0% of runs with a Sandpiper profile · first public 2017-11-03
Authors (23)
Olekhnovich EI first · Manolov AI · Samoilov AE · Prianichnikov NA · Malakhova MV · Tyakht AV · Pavlenko AV · Babenko VV · Larin AK · Kovarsky BA · Starikova EV · Glushchenko OE · Safina DD · Markelova MI · Boulygina EA · Khusnutdinova DR · Malanin SY · Abdulkhakov SR · Abdulkhakov RA · Grigoryeva TV · Kostryukova ES · Govorun VM · Ilina EN last
Downloads
PRJNA413659.csv.gz (3.6 KB) · parquet (75.4 KB) — all 92 samples, every field with route and confidence · PRJNA413659_determinations.csv.gz (9.6 KB) — 1,196 evidence rows