Gut microbiome in COPD vs healthy controls, Newcastle
Case-control study of 95 fecal samples from adults in Newcastle, Australia, comparing COPD patients and healthy controls, with paired metabolomic data generated for the same samples. machine-written summary
95 samples · 95 runs · AU · Adult · 2020 · 2.70 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 646 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11205787, PMC7676259 |
| ✓ Supplementary tables | 135 sample values (medication, subject id) |
| ✓ External resources | 114 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 85 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 | 95 | 100% | ||||
| country | 95 | 100% | 95 | |||
| health_condition | 95 | 100% | 38 | 57 | ||
| subject_id | 95 | 100% | 95 | |||
| collection_date | 95 | 100% | 95 | |||
| detailed_location | 95 | 100% | ||||
| health_condition_detail | 95 | 100% | 38 | 57 | ||
| latitude | 95 | 100% | 95 | |||
| location_locality | 95 | 100% | 95 | |||
| location_region | 95 | 100% | 95 | |||
| longitude | 95 | 100% | 95 | |||
| medication | 40 | 42% | 40 |
- Disease-associated gut microbiome and metabolome changes in patients with chronic obstructive pulmonary disease. 2020 PMID 33208745 PMC7676259 own_data
- Deciphering Microbial Shifts in the Gut and Lung Microbiomes of COVID-19 Patients. 2024 PMID 38930440 PMC11205787 unsure
Archive description
Study analysed metagenomes derived from fecal samples from 28 individuals with chronic obstructive pulmonary disease (COPD) and 29 healthy controls. Paired metabolomic data was also generated for the same samples.
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 · “Fecal microbiome analysis of”
- body site study.description · “metagenomes derived from fecal samples from 28”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN12649817 | collection_date | 2015-05 | R1 | 0.90 | biosample.attribute:collection_date | 2015-05 |
| SAMN12649817 | country | AU | R1 | 0.90 | sample.attr.geo_loc_name | Australia: Newcastle |
| SAMN15889603 | health_condition | other_disease | R1 | 0.70 | sample.name_rule:sample_description | VC09 |
| SAMN12649817 | health_condition | other_disease | R2 | 0.75 | external.gmrepo source | phenotype: Pulmonary Disease, Chronic Obstructive |
| SAMN15889603 | health_condition_detail | VC | R1 | 0.70 | sample.name_rule:sample_description | VC09 |
| SAMN12649817 | health_condition_detail | Pulmonary Disease, Chronic Obstructive | R2 | 0.75 | external.gmrepo source | phenotype: Pulmonary Disease, Chronic Obstructive |
| SAMN12649817 | latitude | -32.9300 | R1 | 0.90 | biosample.attribute:lat_lon | 32.93 S 151.78 E |
| SAMN12649817 | location_locality | Newcastle | R1 | 0.85 | biosample.attribute:geo_loc_name | Australia: Newcastle |
| SAMN12649817 | location_region | New South Wales | R1 | 0.60 | biosample.attribute:lat_lon | 32.93 S 151.78 E |
| SAMN12649817 | longitude | 151.7800 | R1 | 0.90 | biosample.attribute:lat_lon | 32.93 S 151.78 E |
| SAMN12649818 | medication | other_medication | R2 | 0.85 | paper.supp.41467_2020_19701_MOESM5_ESM.xlsx[Supp. Data 2!Beta-agonist (SABA/LABA)] | C03: Beta-agonist (SABA/LABA)=Y Anticholinergic/ muscarinic antagonist (LAMA)=Y |
| SAMN12649817 | subject_id | C01 | R2 | 0.85 | paper.supp.41467_2020_19701_MOESM5_ESM.xlsx[Supp. Data 28!ID] | SAMN12649817: ID=C01 |
Sequencing
95 runs over 95 samples · mean 3.54 Gbp per run (median 2.70 Gbp, total 335.88 Gbp; 95 runs with a base count) · layout PAIRED 95 · platform ILLUMINA 95 · models NextSeq 500 (57), Illumina NovaSeq 6000 (38) · 89% of runs with a Sandpiper profile · first public 2020-10-09 – 2021-07-22
Authors (51)
Bowerman KL first · Rehman SF · Vaughan A · Lachner N · Budden KF · Kim RY · Wood DLA · Gellatly SL · Shukla SD · Wood LG · Yang IA · Wark PA · Hugenholtz P · Hansbro PM last · Zeng S first · Patangia D · Almeida A · Zhou Z · Mu D · Paul Ross R · Stanton C · Wang S last · Fontana F first · Alessandri G · Tarracchini C · Bianchi MG · Rizzo SM · Mancabelli L · Lugli GA · Argentini C · Vergna LM · Anzalone R · Longhi G · Viappiani A · Taurino G · Chiu M · Turroni F · Bussolati O · van Sinderen D · Milani C · Ventura M last · Li S · Ying J · Wang H · Qu Y · Niu X · Pusadkar V first · Mazumder A · Azad A · Patil D · Azad RK last
Downloads
PRJNA562766.csv.gz (3.8 KB) · parquet (75.2 KB) — all 95 samples, every field with route and confidence · PRJNA562766_determinations.csv.gz (8.6 KB) — 895 evidence rows