Microbiome after H. pylori therapy with probiotic milk
539 fecal samples from German adults treated for H. pylori infection, randomised double-blind to a multi-strain fermented milk product or control dairy drink, sampled at four time points up to 4 weeks post-treatment. machine-written summary
539 samples · 539 runs · DE · Adult · 2024 · 9.39 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 4,851 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude, subject id) |
| ✓ Abstract / description | 539 sample values (antibiotic exposure) |
| ○ Full text | read; no usable statement or table · PMC9348039 |
| ○ 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 |
longitudinal
135 of 135 people sampled more than once (539 samples; median 4, up to 4 per person) · follow-up median 42 d (max 42 d) · median interval between samples 14 d (time from timepoint labels). Schedule stated by the source: “Samples collected at four time points: day 0, day 14, day 28, day 42 (up to four weeks after cessation of Hp treatment)” (time origin: intervention_start); stated follow-up 42 d.
Each row is one person (36 shown of 135); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 483 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 | 539 | 100% | ||||
| country | 539 | 100% | 539 | |||
| health_condition | 539 | 100% | 539 | |||
| subject_id | 539 | 100% | 539 | |||
| antibiotic_exposure | 539 | 100% | 539 | |||
| collection_date | 539 | 100% | 539 | |||
| detailed_location | 539 | 100% | ||||
| health_condition_detail | 539 | 100% | 539 | |||
| latitude | 539 | 100% | 539 | |||
| location_region | 539 | 100% | 539 | |||
| longitude | 539 | 100% | 539 | |||
| timepoint_label | 539 | 100% | 539 |
- Improved gut microbiome recovery following drug therapy is linked to abundance and replication of probiotic strains. 2022 PMID 35916669 PMC9348039 unsure
Archive description
In this study, we explored the dynamic of the gut microbiota in a randomised controlled double-blind study, by analysing fecal samples from 136 adults treated for Helicobacter pylori (Hp) infection (14 days Clarithromycin, Amoxicillin and Proton Pump Inhibitor) and concomitantly assigned at random to the consumption of either a multi-strain fermented milk product (FMP) or a control product (acidified dairy drink) twice daily for 28 days. Samples were collected at four time points (up to four weeks after cessation of Hp treatment (D42) (NCT02900196)
How this project entered the registry
Classified as human gut / stool / human milk shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Gut microbiome response to”
- body site study.description · “dynamic of the gut microbiota in a”
- body site study.title · “to a fermented milk product in subjects”
- body site study.description · “a multi-strain fermented milk product (FMP) or”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.description · “samples from 136 adults treated for Helicobacter”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA13912951 | antibiotic_exposure | yes | R4 | 0.50 | study.description | 14 days Clarithromycin, Amoxicillin and Proton Pump Inhibitor |
| SAMEA13912951 | collection_date | 2017-08-03 | R1 | 0.90 | biosample.attribute:collection_date | 2017-08-03 |
| SAMEA13912951 | country | DE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Germany |
| SAMEA13912951 | health_condition | gi_infection_or_diarrhoea | R1 | 0.90 | biosample_attr | Helicobacter pylori |
| SAMEA13912951 | health_condition_detail | Helicobacter pylori | R1 | 0.90 | sample.attr.gastrointestinal_tract_disorder | Helicobacter pylori |
| SAMEA13912951 | latitude | 48.1300 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 48.13 11.57 |
| SAMEA13912951 | location_region | Bavaria | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 48.13 11.57 |
| SAMEA13912951 | longitude | 11.5700 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 48.13 11.57 |
| SAMEA13912951 | subject_id | FITZ_MFZG8337 | R1 | 0.85 | sample.attr.host_subject_id | FITZ_MFZG8337 |
| SAMEA13912951 | timepoint_label | day 0 | R1 | 0.70 | sample.name_rule:library_names | FITZ_MFZG8337_D0 |
Sequencing
539 runs over 539 samples · mean 9.52 Gbp per run (median 9.39 Gbp, total 5,129.55 Gbp; 539 runs with a base count) · layout PAIRED 539 · platform ILLUMINA 539 · models Illumina NovaSeq 6000 (539) · 90% of runs with a Sandpiper profile · first public 2024-04-03
Authors (9)
FitzGerald J first · Patel S · Eckenberger J · Guillemard E · Veiga P · Schäfer F · Walter J · Claesson MJ · Derrien M last
Downloads
PRJEB52093.csv.gz (15.6 KB) · parquet (90.6 KB) — all 539 samples, every field with route and confidence · PRJEB52093_determinations.csv.gz (33.4 KB) — 5,390 evidence rows