Pediatric CF gut microbiome before/after ELX/TEZ/IVA
114 fecal samples from children (plus some adolescents/adults) with cystic fibrosis in Nashville, TN, studying the intestinal microbiome before and after CFTR modulator (ELX/TEZ/IVA) drug therapy in a longitudinal design. machine-written summary
114 samples · 114 runs · US · Age unknown · 2023 · 3.82 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 912 sample values (collection date, country, latitude, location locality, location region, longitude, sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 114 sample values (location site) · PMC10865789 |
| ✓ Supplementary tables | 570 sample values (age, antibiotic exposure, health condition, health condition detail, timepoint) |
| – 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 not resolved
Non-antibiotic pharmaceutical given as the study intervention (metformin design single_arm_before_after · population other_disease · Elexacaftor-tezacaftor-ivacaftor (ELX/TEZ/IVA) CFTR modulator therapy
“effect of ELX/TEZ/IVA on the intestinal microbiome” — abstract:38275294 (study level; per-sample arms are in the intervention column below)
longitudinal
39 of 39 people sampled more than once (114 samples; median 3, up to 4 per person) · follow-up median 3.6 y (max 4.7 y) · median interval between samples 12 mo (time from age at collection). Schedule stated by the source: “Up to 4 stool timepoints/patient: T1/T2 before ELX/TEZ/IVA (median ~33.6 and ~0.64 months before), T3/T4 at ~6 and ~12 months after initiation” (time origin: intervention_start).
Each row is one person (36 shown of 39); 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 | 114 | 100% | ||||
| country | 114 | 100% | 114 | |||
| health_condition | 114 | 100% | 114 | |||
| subject_id | 114 | 100% | 114 | |||
| age_at_collection_days | 114 | 100% | 114 | |||
| antibiotic_exposure | 114 | 100% | 114 | |||
| collection_date | 114 | 100% | 114 | |||
| detailed_location | 114 | 100% | ||||
| health_condition_detail | 114 | 100% | 114 | |||
| latitude | 114 | 100% | 114 | |||
| location_locality | 114 | 100% | 114 | |||
| location_region | 114 | 100% | 114 | |||
| location_site | 114 | 100% | 114 | |||
| longitude | 114 | 100% | 114 | |||
| sex | 114 | 100% | 114 | |||
| timepoint_label | 114 | 100% | 114 |
- Longitudinal profiling of the intestinal microbiome in children with cystic fibrosis treated with elexacaftor-tezacaftor-ivacaftor. 2024 PMID 38275294 PMC10865789 own_data
Archive description
CF patient fecal microbiomes after trikafta therapy
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.73. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN33906609 | age_at_collection_days | 3762 | R2 | 0.80 | paper.supp.mbio.01935-23-s0001.xlsx[metadata!Age] | 10.3 |
| SAMN33906609 | antibiotic_exposure | yes | R2 | 0.80 | paper.supp.mbio.01935-23-s0001.xlsx[metadata!RecentAbx_binary] | Y |
| SAMN33906609 | collection_date | 2021 | R1 | 0.90 | biosample.attribute:collection_date | 2021 |
| SAMN33906609 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Nashville, TN |
| SAMN33906609 | health_condition | other_disease | R2 | 0.80 | paper.supp.mbio.01935-23-s0001.xlsx[metadata!host phenotype] | cystic fibrosis |
| SAMN33906609 | health_condition_detail | cystic fibrosis | R2 | 0.80 | paper.supp.mbio.01935-23-s0001.xlsx[metadata!host phenotype] | cystic fibrosis |
| SAMN33906609 | latitude | 36.1400 | R1 | 0.90 | biosample.attribute:lat_lon | 36.14 N 86.80 W |
| SAMN33906609 | location_locality | Nashville | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Nashville, TN |
| SAMN33906609 | location_region | Tennessee | R1 | 0.75 | biosample.attribute:geo_loc_name | USA: Nashville, TN |
| SAMN33906609 | location_site | Monroe Carell Jr. Children's Hospital at Vanderbilt | R3 | 0.70 | paper.fulltext.methods | Monroe Carell Jr. Children’s Hospital at Vanderbilt (MCJCHV) were recruited |
| SAMN33906609 | longitude | -86.8000 | R1 | 0.90 | biosample.attribute:lat_lon | 36.14 N 86.80 W |
| SAMN33906609 | sex | male | R1 | 0.70 | sample.name_rule:description | Male, 10.3 years old, timepoint 2 |
| SAMN33906609 | subject_id | P10 | R1 | 0.70 | sample.name_rule:alias | V_P10T2 |
| SAMN33906609 | timepoint_label | 2 | R2 | 0.80 | paper.supp.mbio.01935-23-s0001.xlsx[metadata!TimePoint] | 2 |
Sequencing
114 runs over 114 samples · mean 3.97 Gbp per run (median 3.82 Gbp, total 453.10 Gbp; 114 runs with a base count) · layout PAIRED 114 · platform ILLUMINA 114 · models NextSeq 500 (114) · 89% of runs with a Sandpiper profile · first public 2023-12-21 – 2023-12-24
Authors (11)
Reasoner SA first · Bernard R · Waalkes A · Penewit K · Lewis J · Sokolow AG · Brown RF · Edwards KM · Salipante SJ · Hadjifrangiskou M · Nicholson MR last
Downloads
PRJNA948536.csv.gz (4.9 KB) · parquet (77.2 KB) — all 114 samples, every field with route and confidence · PRJNA948536_determinations.csv.gz (12.7 KB) — 1,596 evidence rows