Adult CF vs healthy control stool metagenomes, Brisbane
35 faecal metagenome samples from adult cystic fibrosis patients (19) and healthy controls (16) at Brisbane Mater, Australia, in a case-control study of CF-associated gut microbiome disruption. machine-written summary
35 samples · 35 runs · AU · Adult · 2019 · 2.25 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 451 sample values (age, collection date, country, health condition, health condition detail, latitude, location locality, location region) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC12390848, PMC6546330 |
| ○ 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 33 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 | 35 | 100% | ||||
| country | 35 | 100% | 35 | |||
| health_condition | 35 | 100% | 35 | |||
| subject_id | 35 | 100% | 35 | |||
| collection_date | 35 | 100% | 35 | |||
| detailed_location | 35 | 100% | ||||
| health_condition_detail | 35 | 100% | 35 | |||
| latitude | 35 | 100% | 35 | |||
| location_locality | 35 | 100% | 35 | |||
| location_region | 35 | 100% | 35 | |||
| location_site | 35 | 100% | 35 | |||
| longitude | 35 | 100% | 35 | |||
| timepoint_label | 35 | 100% | 35 | |||
| age_at_collection_days | 33 | 94% | 33 | |||
| sex | 33 | 94% | 33 |
- Opportunistic bacteria confer the ability to ferment prebiotic starch in the adult cystic fibrosis gut. 2019 PMID 30359203 PMC6546330 own_data
- Microbiota-driven antitumour immunity mediated by dendritic cell migration. 2025 PMID 40659786 PMC12390848 unsure
Archive description
Cystic fibrosis (CF) results in altered mucus and chronic respiratory infections, resulting in a high antibiotic burden. Both altered mucus and antibiotics lead to chronic intestinal dysbiosis. This project aimed to explore the extent of microbiome perturbation in CF.
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_adult_only”
- body site study.title · “CF and control stool”
- body site study.description · “lead to chronic intestinal dysbiosis. This project”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.title · “Metagenomic analysis of adult CF and control”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN08779742 | age_at_collection_days | 9562.5 | R1 | 0.85 | sample.attr.host_age | 26.2 |
| SAMN08779742 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMN08779742 | country | AU | R1 | 0.90 | sample.attr.geo_loc_name | Australia: Brisbane Mater |
| SAMN08779742 | health_condition | other_disease | R1 | 0.95 | biosample_attr | Cystic fibrosis |
| SAMN08779744 | health_condition | other_disease | R1 | 0.90 | sample.attr.host_phenotype | Cystic fibrosis |
| SAMN08779742 | health_condition_detail | Cystic fibrosis | R1 | 0.90 | sample.attr.host_phenotype | Cystic fibrosis |
| SAMN08779742 | latitude | -27.4853 | R1 | 0.90 | biosample.attribute:lat_lon | 27.485346 S 153.028320 E |
| SAMN08779742 | location_locality | Brisbane | R1 | 0.85 | biosample.attribute:geo_loc_name | Australia: Brisbane Mater |
| SAMN08779742 | location_region | Queensland | R1 | 0.60 | biosample.attribute:lat_lon | 27.485346 S 153.028320 E |
| SAMN08779742 | location_site | Brisbane Mater | R1 | 0.85 | biosample.attribute:geo_loc_name | Australia: Brisbane Mater |
| SAMN08779742 | longitude | 153.0283 | R1 | 0.90 | biosample.attribute:lat_lon | 27.485346 S 153.028320 E |
| SAMN08779742 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN08779742 | subject_id | GUT001 | R1 | 0.85 | sample.attr.host_subject_id | GUT001 |
| SAMN08779742 | timepoint_label | D0 | R1 | 0.70 | sample.name_rule:alias | G01_D0 |
Sequencing
35 runs over 35 samples · mean 2.31 Gbp per run (median 2.25 Gbp, total 80.84 Gbp; 35 runs with a base count) · layout PAIRED 35 · platform ILLUMINA 35 · models Illumina HiSeq 2500 (35) · 94% of runs with a Sandpiper profile · first public 2019-04-02
Authors (69)
Wang Y first · Leong LEX · Keating RL · Kanno T · Abell GCJ · Mobegi FM · Choo JM · Wesselingh SL · Mason AJ · Burr LD · Rogers GB last · Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last · Ormaasen I first · Rudi K · Diep DB · Snipen L last · De Biase R · Bocchio F · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · van Sinderen D · Lin NY first · Fukuoka S · Koyama S · Motooka D · Tourlousse DM · Shigeno Y · Matsumoto Y · Yamano H · Murotomi K · Tamaki H · Irie T · Sugiyama E · Kumagai S · Itahashi K · Tanegashima T · Fujimaki K · Ito S · Shindo M · Tsuji T · Wake H · Watanabe K · Maeda Y · Enokida T · Tahara M · Yamashita R · Fujisawa T · Nomura M · Kawazoe A · Goto K · Doi T · Shitara K · Mano H · Sekiguchi Y · Nakamura S · Benno Y · Nishikawa H last
Downloads
PRJNA438847.csv.gz (2.2 KB) · parquet (72.6 KB) — all 35 samples, every field with route and confidence · PRJNA438847_determinations.csv.gz (4.1 KB) — 451 evidence rows