Pouchitis antibiotic therapy and gut microbiome, Tel-Aviv
Longitudinal study of 234 fecal samples from pouchitis/pouch patients in Tel-Aviv, Israel, examining gut microbiome changes associated with antibiotic (ciprofloxacin/metronidazole) treatment response and antibiotic dependence. machine-written summary
234 samples · 234 runs · IL · Age unknown · 2019 · 1.00 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,404 sample values (collection date, country, latitude, location locality, location region, longitude) |
| ✓ Abstract / description | 139 sample values (health condition detail) |
| ○ Full text | read; no usable statement or table · PMC8546988 |
| ✓ Supplementary tables | 559 sample values (age, health condition, health condition detail, sex, subject id) |
| – 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
32 of 40 people sampled more than once (115 samples; median 3, up to 12 per person) · follow-up median 2.2 y (max 5.8 y) · median interval between samples 8 mo (time from age at collection). Schedule stated by the source: “Fecal samples (n=234) collected over time during or absent antibiotic treatment; 40 subjects, median 3 samples/subject (max 12)”.
Each row is one person (32 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 101 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 | 123 | 53% | ||||
| country | 234 | 100% | 234 | |||
| health_condition | 95 | 41% | 95 | |||
| subject_id | 123 | 53% | 123 | |||
| collection_date | 234 | 100% | 234 | |||
| detailed_location | 234 | 100% | ||||
| health_condition_detail | 234 | 100% | 95 | 139 | ||
| latitude | 234 | 100% | 234 | |||
| location_locality | 234 | 100% | 234 | |||
| location_region | 234 | 100% | 234 | |||
| longitude | 234 | 100% | 234 | |||
| age_at_collection_days | 123 | 53% | 123 | |||
| sex | 123 | 53% | 123 |
- Predominantly Antibiotic-resistant Intestinal Microbiome Persists in Patients With Pouchitis Who Respond to Antibiotic Therapy. 2020 PMID 31605691 own_data
- Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-anal Pouch Resembles That Observed in Crohn's Disease. 2021 PMID 33653942 PMC8546988 unsure
Archive description
Pouchitis developing after total proctocolectomy and ileal pouch anal anastomosis in patients with ulcerative colitis is usually treated with antibiotics. Patients often develop antibiotic dependent or refractory disease and may be treated with antibiotics for prolonged periods. The mechanisms of response to antibiotic treatment in pouchitis and the effects on bacterial communities are mostly unknown. In this study we investigated the microbial factors that underlie the response to antibiotic treatment for pouchitis and why patients tend to develop antibiotic dependence.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.80. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “feces metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11023869 | age_at_collection_days | 25020.0 | R2 | 0.85 | paper.supp.msystems.00984-20-sd001.xlsx[Data Set S1-sheet1 - Metadata for Pouch patients cohort (discovery)!Age (relative to sample)] | L7: Age (relative to sample)=68.5 |
| SAMN11023868 | collection_date | 2013-01-10 | R1 | 0.90 | biosample.attribute:collection_date | 2013-01-10 |
| SAMN11023868 | country | IL | R1 | 0.90 | sample.attr.geo_loc_name | Israel: Tel-Aviv |
| SAMN11023869 | health_condition | healthy_control | R2 | 0.85 | paper.supp.msystems.00984-20-sd001.xlsx[Data Set S1-sheet1 - Metadata for Pouch patients cohort (discovery)!Pouch_phenotype (disease behavior)] | L7: Pouch_phenotype (disease behavior)=Normal pouch |
| SAMN11023869 | health_condition_detail | Pouch_phenotype (disease behavior): Normal pouch | R2 | 0.85 | paper.supp.msystems.00984-20-sd001.xlsx[Data Set S1-sheet1 - Metadata for Pouch patients cohort (discovery)!Pouch_phenotype (disease behavior)] | L7: Pouch_phenotype (disease behavior)=Normal pouch |
| SAMN11023868 | health_condition_detail | mixed_case_control: pouchitis patients (recurrent-acute, chronic, Crohn's-like) vs normal pouch controls | R4 | 0.50 | study.description | Pouchitis developing after total proctocolectomy |
| SAMN11023868 | latitude | 32.0806 | R1 | 0.90 | biosample.attribute:lat_lon | 32.0806 N 34.7898 E |
| SAMN11023868 | location_locality | Tel Aviv | R1 | 0.75 | biosample.attribute:geo_loc_name | Israel: Tel-Aviv |
| SAMN11023868 | location_region | Tel Aviv | R1 | 0.60 | biosample.attribute:lat_lon | 32.0806 N 34.7898 E |
| SAMN11023868 | longitude | 34.7898 | R1 | 0.90 | biosample.attribute:lat_lon | 32.0806 N 34.7898 E |
| SAMN11023869 | sex | female | R2 | 0.85 | paper.supp.msystems.00984-20-sd001.xlsx[Data Set S1-sheet1 - Metadata for Pouch patients cohort (discovery)!Gender] | L7: Gender=Female |
| SAMN11023869 | subject_id | po58 | R2 | 0.85 | paper.supp.msystems.00984-20-sd001.xlsx[Data Set S1-sheet1 - Metadata for Pouch patients cohort (discovery)!Patient_ID] | L7: Patient_ID=po58 |
Sequencing
234 runs over 234 samples · mean 0.99 Gbp per run (median 1.00 Gbp, total 232.22 Gbp; 234 runs with a base count) · layout PAIRED 234 · platform ILLUMINA 234 · models NextSeq 500 (234) · 44% of runs with a Sandpiper profile · first public 2019-10-22
Authors (20)
Dubinsky V first · Reshef L · Bar N · Keizer D · Golan N · Rabinowitz K · Godny L · Yadgar K · Zonensain K · Tulchinsky H · Gophna U · Dotan I last · Wasserberg N · Rozman V first · Mohar Lorbeg P · Treven P · Accetto T · Golob M · Zdovc I · Bogovič Matijašić B last
Downloads
PRJNA524170.csv.gz (8.6 KB) · parquet (82.4 KB) — all 234 samples, every field with route and confidence · PRJNA524170_determinations.csv.gz (21.1 KB) — 2,102 evidence rows