E. coli genomics in IBD patients, Tel-Aviv, cross-sectional
Cross-sectional study of 58 fecal metagenome samples from Tel-Aviv, Israel, comparing E. coli genomic adaptations among healthy controls, ulcerative colitis and other patient groups. machine-written summary
58 samples · 58 runs · IL · Age unknown · 2022 · 5.50 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 464 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 45 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 | 0 | 0% | ||||
| country | 58 | 100% | 58 | |||
| health_condition | 58 | 100% | 58 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 58 | 100% | 58 | |||
| detailed_location | 58 | 100% | ||||
| health_condition_detail | 58 | 100% | 58 | |||
| latitude | 58 | 100% | 58 | |||
| location_locality | 58 | 100% | 58 | |||
| location_region | 58 | 100% | 58 | |||
| longitude | 58 | 100% | 58 |
- Escherichia coli Strains from Patients with Inflammatory Bowel Diseases have Disease-specific Genomic Adaptations. 2022 PMID 35560165 own_data
Archive description
Comparative genomic study of E. coli from fecal metagenomes of patients with IBD, revealing lineages with different metabolic capabilites and disease-specific adaptations.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.78. 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 |
|---|---|---|---|---|---|---|
| SAMN19238734 | collection_date | 2012-03-04 | R1 | 0.90 | biosample.attribute:collection_date | 2012-03-04 |
| SAMN19238734 | country | IL | R1 | 0.90 | sample.attr.geo_loc_name | Israel: Tel-Aviv |
| SAMN19238734 | health_condition | healthy_control | R1 | 0.80 | biosample_attr | Normal |
| SAMN19238736 | health_condition | ulcerative_colitis | R1 | 0.85 | biosample.attribute:gastrointest_disord | Patient with a pouch (former UC) |
| SAMN19238734 | health_condition_detail | Normal | R1 | 0.90 | sample.attr.host_phenotype | Normal |
| SAMN19238734 | latitude | 32.0806 | R1 | 0.90 | biosample.attribute:lat_lon | 32.0806 N 34.7898 E |
| SAMN19238734 | location_locality | Tel Aviv | R1 | 0.75 | biosample.attribute:geo_loc_name | Israel: Tel-Aviv |
| SAMN19238734 | location_region | Tel Aviv | R1 | 0.60 | biosample.attribute:lat_lon | 32.0806 N 34.7898 E |
| SAMN19238734 | longitude | 34.7898 | R1 | 0.90 | biosample.attribute:lat_lon | 32.0806 N 34.7898 E |
Sequencing
58 runs over 58 samples · mean 4.64 Gbp per run (median 5.50 Gbp, total 268.99 Gbp; 58 runs with a base count) · layout PAIRED 58 · platform ILLUMINA 58 · models NextSeq 500 (58) · 78% of runs with a Sandpiper profile · first public 2022-01-01
Authors (0)
No author record.
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJNA730677.csv.gz (2.7 KB) · parquet (72.3 KB) — all 58 samples, every field with route and confidence · PRJNA730677_determinations.csv.gz (4.0 KB) — 464 evidence rows