Gut microbiota in H. pylori before/after antibiotics, Russia
10 stool samples from Russian patients with Helicobacter pylori infection, collected before and after antibiotic eradication therapy (and 1 month later for two subjects), analyzed by shotgun metagenomic sequencing. machine-written summary
10 samples · 10 runs · RU · Age unknown · 2016 · 9.26 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 40 sample values (collection date, country, latitude, longitude) |
| ✓ Abstract / description | 10 sample values (antibiotic exposure) |
| ✓ Full text | 18 sample values (age, location site, sex) · PMC5256668 |
| ○ 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 gi_infection_or_diarrhoea · Quadruple H. pylori eradication antibiotic therapy, pre/post sampling
“before and after the antibiotic therapy” — abstract:28138506 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
Schedule stated by the source: “Samples taken before and directly after H. pylori eradication therapy; for 2 of 4 subjects, an additional sample 1 month later.”; stated follow-up 30 d.
Genera, mean relative abundance over 7 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 | 4 | 40% | ||||
| country | 10 | 100% | 10 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 10 | 100% | 10 | |||
| collection_date | 10 | 100% | 10 | |||
| detailed_location | 10 | 100% | ||||
| latitude | 10 | 100% | 10 | |||
| location_site | 10 | 100% | 10 | |||
| longitude | 10 | 100% | 10 | |||
| age_at_collection_days | 4 | 40% | 4 | |||
| sex | 4 | 40% | 4 |
- Data on gut metagenomes of the patients with Helicobacter pylori infection before and after the antibiotic therapy. 2017 PMID 28138506 PMC5256668 own_data
- Shifts in the Human Gut Microbiota Structure Caused by Quadruple Helicobacter pylori Eradication Therapy. 2019 PMID 31507546 PMC6718723 unsure
- Quantifying and Cataloguing Unknown Sequences within Human Microbiomes. 2022 PMID 35258340 PMC9052204 unsure
Archive description
A problem of antibiotic resistance emergence in microbiome will be investigated in the research. To date, gut microbiome (as well as soil microbiome) is considered to be antibiotic resistance reservoir. The resistance can accumulate in the microbiome after antibiotic treatment against infectious agents, and it can be passed to pathogenic bacteria during further infections, even though absence of the target infection is checked after each therapy. Moreover, use of antibiotics in agriculture and every day life (without doctor’s recommendations) creates an environment for antibiotic resistance transfer between microbiomes, as there is always a selective pressure for it. That is a quite dangerous situation, as there is a permanent ubiquitous antibiotic resistance (AR) background. In the framework of the research available data on Russian and worldwide microbiomes (more than 2000 by 2015 year) will be analyzed and groups of patients who passed antibiotic treatment will be studied. Using obtained results a map of antibiotic resistance expansion will be created, dominating mechanisms of the resistance transfer and AR genes hosts will be revealed. Additionally, laboratory methods and mathematical analysis for genes’ and mechanisms’ screening will be developed. The developed models AR transfer will make possible modeling of various methods for AR transfer prevention, or, alternatively, modeling of consequences of different antibiotics’ use. Concluding, basic mechanisms of AR emergence will be described (6-1-3) and new methods of screening will be proposed. Furthermore, principle of the screening operation will be demonstrated on available data on AR, as well as on chosen clinical groups.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.70. Assay shotgun_dna.
- host study.title · “gut microbiota resistome of the Russian citizens”
- body site study.title · “gut microbiota resistome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA17973418 | age_at_collection_days | 11323.0 | R3 | 0.85 | paper.body.Table 1[Age] | Hp_21_S2: 31 |
| SAMEA17973418 | antibiotic_exposure | yes | R4 | 0.50 | paper.abstract | directly after the H. pylori eradication course |
| SAMEA17973418 | collection_date | 2015 | R1 | 0.90 | biosample.attribute:collection_date | 2015 |
| SAMEA17973418 | country | RU | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Russia |
| SAMEA17973418 | latitude | 55.7833 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | N55°47 E49°06 |
| SAMEA17973418 | location_site | University Hospital of Kazan Federal University | R3 | 0.70 | paper.fulltext.methods | enrolled in University Hospital of Kazan Federal University |
| SAMEA17973418 | longitude | 49.1000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | N55°47 E49°06 |
| SAMEA17973418 | sex | male | R3 | 0.85 | paper.body.Table 1[Gender] | Hp_21_S2: M |
Sequencing
10 runs over 10 samples · mean 8.76 Gbp per run (median 9.26 Gbp, total 87.63 Gbp; 10 runs with a base count) · layout PAIRED 10 · platform ILLUMINA 10 · models Illumina HiSeq 2500 (10) · 70% of runs with a Sandpiper profile · first public 2016-11-30
Authors (28)
Glushchenko OE first · Samoilov AE · Olekhnovich EI · Kovarsky BA · Tyakht AV · Pavlenko AV · Babenko VV · Larin AK · Kostryukova ES · Malakhova MV · Ilina EN · Abdulkhakov RA · Safina DI · Grigoryeva TV · Abdulkhakov SR · Govorun VM last · Manolov AI · Prianichnikov NA · Starikova EV · Safina DD · Markelova MI · Boulygina EA · Khusnutdinova DR · Malanin SY · Modha S first · Robertson DL · Hughes J · Orton RJ last
Downloads
PRJEB18265.csv.gz (1.2 KB) · parquet (70.5 KB) — all 10 samples, every field with route and confidence · PRJEB18265_determinations.csv.gz (1.2 KB) — 68 evidence rows