Fecal microbiota in adults with CF before/after ETI therapy
345 fecal samples from adults with cystic fibrosis (124 participants) in the multicenter PROMISE study, analyzed longitudinally before and after elexacaftor/tezacaftor/ivacaftor (ETI) therapy to relate microbiota changes to fecal calprotectin and CFTR genotype. machine-written summary
345 samples · 345 runs · US · Adult · 2025 · 7.56 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,158 sample values (health condition, health condition detail, intervention, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 912 sample values (country, health condition, health condition detail) · PMC12393131 |
| – 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention · arms resolved
Non-antibiotic pharmaceutical given as the study intervention (metformin design single_arm_before_after · population other_disease · CFTR modulator elexacaftor/tezacaftor/ivacaftor (ETI), before/1mo/6mo after
“before, 1-month post, and 6-months post ETI” — abstract:40483244 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
124 of 124 people sampled more than once (345 samples; median 3, up to 3 per person). Schedule stated by the source: “Samples collected pre-ETI (baseline), 1 month post-ETI, and 6 months post-ETI initiation”; stated follow-up 6 mo.
Genera, mean relative abundance over 336 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 | 345 | 100% | ||||
| country | 345 | 100% | 345 | |||
| health_condition | 345 | 100% | 30 | 315 | ||
| subject_id | 345 | 100% | 345 | |||
| health_condition_detail | 345 | 100% | 93 | 252 | ||
| intervention | 345 | 100% | 345 | |||
| timepoint_label | 345 | 100% | 345 |
- Fecal microbiota changes in people with cystic fibrosis after 6 months of elexacaftor/tezacaftor/ivacaftor: Findings from the promise study 2025 PMID 40483244 PMC12393131 own_data
Archive description
Cystic fibrosis (CF) gastrointestinal (GI) disease carries a significant disease burden, inclusive of intestinal obstruction, pancreatic insufficiency, and CF hepatobiliary involvement. While the pathogenesis of these GI manifestations remains unknown, there is a postulated role for intestinal inflammation in driving CF GI disease. People with CF often have fecal dysbioses relative to healthy individuals without CF characterized by increased abundances of pro-inflammatory microbiota correlating with increased fecal measures of inflammation as measured by fecal calprotectin. Findings from the prospective, multi-center observational PROMISE study showed that treatment with the CFTR modulator elexacaftor/tezacaftor/ivacaftor (ETI) is followed by a decrease in fecal calprotectin. However, it is unknown how ETI changes the composition of the fecal microbiota and how such changes relate to fecal calprotectin, which is critical to understanding the pathogenesis of CF related GI disease. We analyzed fecal samples from PROMISE to define the relationships between dysbiosis and inflammatory measures before and after ETI.
How this project entered the registry
Classified as human gut / stool 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_unknown_no_evidence”
- body site study.title · “Changes in Fecal Microbiota in Adults”
- body site study.description · “Cystic fibrosis (CF) gastrointestinal (GI) disease carries”
- life stage study.title · “Fecal Microbiota in Adults with Cystic Fibrosis”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN44592553 | country | US | R3 | 0.70 | paper.fulltext.methods | Fifty-six US CF Foundation-accredited Care Centers |
| SAMN44592589 | health_condition | liver_disease | R1 | 0.70 | biosample_attr | aCFLD |
| SAMN44592553 | health_condition | other_disease | R3 | 0.70 | paper.fulltext.methods | PwCF ages ≥12 y/o with at least one F508del allele |
| SAMN44592577 | health_condition_detail | CFnoLD | R1 | 0.90 | sample.attr.cf_liver_disease | CFnoLD |
| SAMN44592553 | health_condition_detail | PwCF ages ≥12 y/o with at least one F508del allele in the CFTR gene | R3 | 0.70 | paper.fulltext.methods | PwCF ages ≥12 y/o with at least one F508del allele |
| SAMN44592553 | intervention | drug_therapy | R1 | 0.70 | sample.name_rule:alias | P0033 _1moETI |
| SAMN44592553 | subject_id | P0033 | R1 | 0.70 | sample.name_rule:alias | P0033 _1moETI |
| SAMN44592553 | timepoint_label | 1moETI | R1 | 0.70 | sample.name_rule:alias | P0033 _1moETI |
Sequencing
345 runs over 345 samples · mean 8.02 Gbp per run (median 7.56 Gbp, total 2,766.23 Gbp; 345 runs with a base count) · layout PAIRED 345 · platform ILLUMINA 345 · models NextSeq 2000 (345) · 97% of runs with a Sandpiper profile · first public 2025-06-11 – 2025-06-23
Authors (14)
Duong JT first · Hayden HS · Verster AJ · Pope CE · Miller C · Kelsi Penewit None · Salipante SJ · Rowe SM · Solomon GM · Nichols D · Kelly A · Schwarzenberg SJ · Freedman SD · Hoffman LR last
Downloads
PRJNA1177516.csv.gz (9.7 KB) · parquet (82.2 KB) — all 345 samples, every field with route and confidence · PRJNA1177516_determinations.csv.gz (16.3 KB) — 2,070 evidence rows