Pouch microbiome and resistome in UC patients, Denmark
Case-control study of 605 fecal samples from Denmark comparing healthy ileal pouches, chronic pouchitis, ulcerative colitis, and normal gut microbiomes, examining microbial composition and antimicrobial resistance. machine-written summary
605 samples · 806 runs · DK · Age unknown · 2026 · 3.01 Gbp / sample
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what each source gave
| ✓ Sequence archive | 1,210 sample values (collection date, country) |
| – Abstract / description | no abstract or project description |
| – 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 |
intervention — arms not resolved
design observational_with_procedure
Genera, mean relative abundance over 443 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 | 605 | 100% | 605 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 605 | 100% | 605 |
Archive description
Background Fecal matter transplantation (FMT) from donors with a healthy functioning colon has been investigated for its potential use in treating chronic pouchitis, with limited effect. However, what constitutes a normal functioning ileal pouch-anal anastomosis (IPAA) (healthy) pouch microbiome is unknown. We investigated the microbial characteristics of a healthy IPAA (HealthyPouch) compared with chronic pouchitis (SickPouch), ulcerative colitis (UC), and a normal gut microbiome (NormalGut). Furthermore, we investigated how repeated antibiotic use influences antimicrobial resistance on a genome level. Methods Fecal samples from 191 participants were collected HealthyPouch (n=38), SickPouch (n=38), UC (n=23), and NormalGut (n=92) and sequenced with Illumina and taxonomically profiled with MetaPhlAn4. Samples from HealthyPouch, SickPouch, and NormalGut were also long-read sequenced using Oxford Nanopore Technologies for metagenome-assembled genome (MAG) reconstruction. Findings The HealthyPouch microbiome is distinct from both the UC and NormalGut microbiome while significantly more diverse compared to the SickPouch. E. coli MAGs in the SickPouch microbiome had significantly higher prevalence of gyrA and parC mutations conferring resistance in the SickPouch (n=22) microbiome compared to both HealthyPouch (n=25) and NormalGut (n=41) (p<0.0001). Lastly, DNA methylation pattern was used to associate three plasmids to E. coli with extended-spectrum beta lactamase (ESBL) genes. Interpretation HealthyPouch microbiota differs from NormalGut microbiota, and could therefore be more appropriate for FMT treatment of pouchitis. Repeated antibiotic consumption drives shifts in community structure and enriches gyrA/parC resistance mutations in E. coli in the SickPouch group. Using DNA methylation, ESBL carrying plasmids could be associated with E. coli MAGs. These results emphasize the pouch as a unique microbial niche and underscore the need for careful antibiotic use and resistance monitoring.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.57. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.title · “Ileal Pouches in Ulcerative Colitis”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA120295071 | collection_date | 2019-04-11 | R1 | 0.90 | biosample.attribute:collection_date | 2019-04-11 |
| SAMEA120295071 | country | DK | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Denmark |
Sequencing
806 runs over 605 samples · mean 3.68 Gbp per run (median 2.06 Gbp, total 2,964.40 Gbp; 806 runs with a base count) · layout PAIRED 560, SINGLE 246 · platform ILLUMINA 560, OXFORD_NANOPORE 246 · models Illumina NovaSeq 6000 (560), PromethION (246) · 55% of runs with a Sandpiper profile · first public 2026-01-06 – 2026-07-18
Authors (15)
So Y first · Pichler MJ · Kappel SS · Jin C · Eriksen C · Chatzigiannidou I · Andersen MHB · Tsiamis V · Lukassen MV · Skytthe LE · Teneberg S · Kristiansen K · Brix S · Aunsholt L · Abou Hachem M last
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata
Downloads
PRJEB98069.csv.gz (15.5 KB) · parquet (92.5 KB) — all 605 samples, every field with route and confidence · PRJEB98069_determinations.csv.gz (9.0 KB) — 1,210 evidence rows