Gut microbiome, lung cancer cachexia, Budapest
31 stool samples from lung cancer patients in Budapest, Hungary, compared gut microbiome composition and function between those with and without cancer cachexia, in a case-control design. machine-written summary
31 samples · 31 runs · HU · Age unknown · 2021 · 6.12 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 279 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 31 sample values (antibiotic exposure) · PMC8528809, PMC8601557 |
| ✓ Supplementary tables | 61 sample values (age, sex) |
| – 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 26 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 | 30 | 97% | ||||
| country | 31 | 100% | 31 | |||
| health_condition | 31 | 100% | 31 | |||
| subject_id | 31 | 100% | 31 | |||
| antibiotic_exposure | 31 | 100% | 31 | |||
| collection_date | 31 | 100% | 31 | |||
| detailed_location | 31 | 100% | ||||
| health_condition_detail | 31 | 100% | 31 | |||
| latitude | 31 | 100% | 31 | |||
| location_locality | 31 | 100% | 31 | |||
| location_region | 31 | 100% | 31 | |||
| longitude | 31 | 100% | 31 | |||
| sex | 31 | 100% | 31 | |||
| age_at_collection_days | 30 | 97% | 30 |
- Distinct composition and metabolic functions of human gut microbiota are associated with cachexia in lung cancer patients. 2021 PMID 34002024 PMC8528809 own_data
- Gut microbiome functionality might be associated with exercise tolerance and recurrence of resected early-stage lung cancer patients. 2021 PMID 34793492 PMC8601557 unsure
Archive description
Cachexia is associated with decreased survival in cancer patients and has a prevalence of up to 80%. In this study, we applied shotgun metagenomics to collected stool samples from lung cancer patients with known cachexia status, aiming for a deeper understanding of the role of human gut microbiome in cachexia under clinical settings.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.85. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.title · “human gut microbiota Raw sequence reads”
- body site study.description · “collected stool samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN19462002 | age_at_collection_days | 22280.0 | R2 | 0.85 | paper.supp.41396_2021_998_MOESM1_ESM.docx[table1!Age] | Age: 61 |
| SAMN19462002 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | no antibiotics usage 60 days prior to stool sample collection |
| SAMN19462002 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMN19462002 | country | HU | R1 | 0.90 | sample.attr.geo_loc_name | Hungary: Budapest |
| SAMN19462002 | health_condition | other_cancer | R1 | 0.85 | biosample.attribute:description | Non-cachexia |
| SAMN19462002 | health_condition_detail | Non-cachexia | R1 | 0.85 | biosample.attribute:description | Non-cachexia |
| SAMN19462002 | latitude | 47.4979 | R1 | 0.90 | biosample.attribute:lat_lon | 47.4979 N 19.0402 E |
| SAMN19462002 | location_locality | Budapest | R1 | 0.85 | biosample.attribute:geo_loc_name | Hungary: Budapest |
| SAMN19462002 | location_region | Budapest | R1 | 0.60 | biosample.attribute:lat_lon | 47.4979 N 19.0402 E |
| SAMN19462002 | longitude | 19.0402 | R1 | 0.90 | biosample.attribute:lat_lon | 47.4979 N 19.0402 E |
| SAMN19462002 | sex | male | R2 | 0.85 | paper.supp.41396_2021_998_MOESM1_ESM.docx[table1!Gender] | Gender: M |
| SAMN19462002 | subject_id | 03MT | R1 | 0.85 | biosample.attribute:TITLE | Subject ID 03MT Non-cachexia |
Sequencing
31 runs over 31 samples · mean 5.88 Gbp per run (median 6.12 Gbp, total 182.14 Gbp; 31 runs with a base count) · layout PAIRED 31 · platform ILLUMINA 31 · models Illumina HiSeq 4000 (31) · 84% of runs with a Sandpiper profile · first public 2021-06-08
Authors (16)
Ni Y first · Lohinai Z · Heshiki Y · Dome B · Moldvay J · Dulka E · Galffy G · Berta J · Weiss GJ · Sommer MOA · Panagiotou G last · Marfil-Sánchez A first · Seelbinder B · Varga J · Hollosi V · Megyesfalvi Z
Downloads
PRJNA626477.csv.gz (1.9 KB) · parquet (71.8 KB) — all 31 samples, every field with route and confidence · PRJNA626477_determinations.csv.gz (3.7 KB) — 371 evidence rows