Airway Microbiome in Cystic Fibrosis Dysglycemia, USA
87 sputum samples from people with cystic fibrosis in the USA, studied in a case-control design comparing airway microbiome and virome across cystic fibrosis-related diabetes, impaired glucose tolerance, and machine-written summary
87 samples · 87 runs · US · Age unknown · 2025 · 15.84 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 522 sample values (collection date, country, latitude, location region, longitude, subject id) |
| ✓ Abstract / description | 87 sample values (health condition detail) |
| ○ Full text | read; no usable statement or table · PMC12503272 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 52 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 | 87 | 100% | 87 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 87 | 100% | 87 | |||
| collection_date | 87 | 100% | 87 | |||
| detailed_location | 87 | 100% | ||||
| health_condition_detail | 87 | 100% | 87 | |||
| latitude | 87 | 100% | 87 | |||
| location_region | 87 | 100% | 87 | |||
| longitude | 87 | 100% | 87 |
- Dysglycemia and the airway microbiome in cystic fibrosis. 2025 PMID 41056240 PMC12503272 unsure
Archive description
This set represents respiratory microbiome samples from people with Cystic Fibrosis Contact: Peggy Lai. This submission was powered by METAGENOTE (https://metagenote.niaid.nih.gov).
How this project entered the registry
Classified as human lower respiratory / gut / stool / oral cavity shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “respiratory microbiome samples from people with Cystic Fibrosis”
- body site sample.attr.env_medium · “human-associated habitat ENVO:00009078 (n=12/87)”
- body site sample.attr.env_medium · “mucus material ENVO:02000063 (n=11/87)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN40023351 | collection_date | 2021-07-01 | R1 | 0.90 | biosample.attribute:collection_date | 2021-07-01 |
| SAMN40023351 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN40023351 | health_condition_detail | mixed_case_control: Cystic fibrosis with dysglycemia (CFRD) vs impaired glucose tolerance (IGT) vs normal glucose tolera | R4 | 0.50 | paper.abstract | 29 with CFRD, 12 with IGT and 22 with NGT |
| SAMN40023351 | latitude | 42.3601 | R1 | 0.90 | biosample.attribute:lat_lon | 42.3601 N 71.0589 W |
| SAMN40023351 | location_region | Massachusetts | R1 | 0.60 | biosample.attribute:lat_lon | 42.3601 N 71.0589 W |
| SAMN40023351 | longitude | -71.0589 | R1 | 0.90 | biosample.attribute:lat_lon | 42.3601 N 71.0589 W |
| SAMN40023351 | subject_id | 1 | R1 | 0.85 | sample.attr.host_subject_id | 1 |
Sequencing
87 runs over 87 samples · mean 17.31 Gbp per run (median 15.84 Gbp, total 1,506.16 Gbp; 87 runs with a base count) · layout PAIRED 87 · platform ILLUMINA 87 · models Illumina NovaSeq 6000 (87) · 98% of runs with a Sandpiper profile · first public 2025-08-27 – 2025-09-21
Authors (9)
Brenner LN first · Huang CY · Kim M · Bringhurst L · Richards CJ · Sicilian L · Neuringer I · Putman MS · Lai PS last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJNA1078869.csv.gz (3.8 KB) · parquet (74.6 KB) — all 87 samples, every field with route and confidence · PRJNA1078869_determinations.csv.gz (5.3 KB) — 609 evidence rows