Gut maturation in infants with cystic fibrosis, NH
Longitudinal cohort of 190 gut microbiome samples from infants and neonates with cystic fibrosis in New Hampshire, USA, studying developmental dynamics and delayed maturation of the gut microbiome. machine-written summary
190 samples · 190 runs · US · Infant / toddler · 2023 · 5.86 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 570 sample values (collection date, country, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11898760, PMC13393419 |
| ✓ Supplementary tables | 378 sample values (age, health condition) |
| ✓ External resources | 191 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 179 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 | 189 | 99% | ||||
| country | 190 | 100% | 190 | |||
| health_condition | 190 | 100% | 190 | |||
| subject_id | 190 | 100% | 190 | |||
| collection_date | 190 | 100% | 190 | |||
| health_condition_detail | 190 | 100% | 190 | |||
| age_at_collection_days | 189 | 99% | 189 |
- Persistent delay in maturation of the developing gut microbiota in infants with cystic fibrosis. PMID 39945545 PMC11898760 curated
- A genotoxin associated with colorectal cancer linked to gut dysbiosis in children with cystic fibrosis. PMID 42262087 PMC13393419 curated
Archive description
Developmental dynamics in the gut microbiome of cystic fibrosis.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “of the developing gut microbiome in infants”
- body site study.description · “dynamics in the gut microbiome of cystic”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “gut microbiome in infants with cystic fibrosis”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN34167669 | age_at_collection_days | 989 | R2 | 0.75 | paper.supp.table | AgeMonth=32.48 |
| SAMN34167668 | collection_date | 2018-01-08 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2018-01-08 |
| SAMN34167668 | country | US | R1 | 0.90 | biosample_attr | USA: New Hampshire |
| SAMN34167668 | health_condition | other_disease | R2 | 0.75 | external.gmrepo source | phenotype: Cystic Fibrosis |
| SAMN34167669 | health_condition | other_disease | R2 | 0.70 | paper.supp.table | Type=CF |
| SAMN34167668 | health_condition_detail | Cystic Fibrosis | R2 | 0.75 | external.gmrepo source | phenotype: Cystic Fibrosis |
| SAMN34167668 | subject_id | 021721_144 | R1 | 0.85 | biosample_attr | 021721_144 |
Sequencing
190 runs over 190 samples · mean 5.78 Gbp per run (median 5.86 Gbp, total 1,098.44 Gbp; 190 runs with a base count) · layout PAIRED 190 · platform ILLUMINA 190 · models NextSeq 550 (190) · 94% of runs with a Sandpiper profile · first public 2023-06-22 – 2023-06-24
Authors (19)
Verster AJ first · Salerno P · Valls R · Barrack K · Price CE · McClure EA · Madan JC · O'Toole GA · Sanville JL · Ross BD last · Barrack KE first · Surve SV · de Sousa Bezerra AV · Murphy CE · Soucy SM · Aguilar Ramos MA · Valls RA · Ruff RD · Balskus EP
Downloads
PRJNA955235.csv.gz (7.7 KB) · parquet (80.9 KB) — all 190 samples, every field with route and confidence · PRJNA955235_determinations.csv.gz (12.3 KB) — 1,139 evidence rows