Gut microbiome method comparison, 9 samples, Spain
Cross-sectional study of 9 samples (paired stool and colon biopsy) from participants in Spain, comparing shotgun and 16S sequencing technologies for gut microbiome analysis; no health condition specified. machine-written summary
9 samples · 9 runs · ES · Age unknown · 2019 · 9.51 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 45 sample values (collection date, country, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 53 sample values (age, health condition, health condition detail, medication, sex, smoking status) · PMC10538363, PMC7075950, PMC9454175 |
| ○ 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 6 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 | 8 | 89% | ||||
| country | 9 | 100% | 9 | |||
| health_condition | 9 | 100% | 9 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 9 | 100% | 9 | |||
| detailed_location | 9 | 100% | ||||
| health_condition_detail | 9 | 100% | 9 | |||
| latitude | 9 | 100% | 9 | |||
| location_region | 9 | 100% | 9 | |||
| longitude | 9 | 100% | 9 | |||
| medication | 9 | 100% | 9 | |||
| sex | 9 | 100% | 9 | |||
| smoking_status | 9 | 100% | 9 | |||
| age_at_collection_days | 8 | 89% | 8 |
- Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample. 2020 PMID 32179734 PMC7075950 own_data
- Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2. 2022 PMID 36076275 PMC9454175 own_data
- Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT. 2023 PMID 37253540 PMC10538363 own_data
Archive description
The human gut microbiome is currently the focus of many research lines given its role in health and disease. However, studies which employ next generation sequencing techniques use different technologies and protocols, which adds to the current reproducibility problem. Here, weobtained colon biopsy and stool samples from nine individuals and sequenced them using shotgun (for feacal samples) and 16S (for matchedfaeces and colon biopsies). 16S data includes reads from different variable regions.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host study.description · “obtained colon biopsy and stool samples from nine individuals”
- body site study.title · “9 stools, sequenced by shotgun”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA5767131 | age_at_collection_days | 22646.0 | R3 | 0.80 | paper.body.Table 2[Age] | 62 |
| SAMEA5767131 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMEA5767131 | country | ES | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Spain |
| SAMEA5767131 | health_condition | colorectal_adenoma | R3 | 0.80 | paper.body.Table 2[Condition] | HRA |
| SAMEA5767131 | health_condition_detail | HRA | R3 | 0.80 | paper.body.Table 2[Condition] | HRA |
| SAMEA5767131 | latitude | 41.3447 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 41°20'40.9"N 2°06'37.3"E |
| SAMEA5767131 | location_region | Catalonia | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 41°20'40.9"N 2°06'37.3"E |
| SAMEA5767131 | longitude | 2.1104 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 41°20'40.9"N 2°06'37.3"E |
| SAMEA5767131 | medication | none_reported | R3 | 0.80 | paper.body.Table 1[NSAIDS use] | No |
| SAMEA5767131 | sex | male | R3 | 0.80 | paper.body.Table 2[Sex] | Male |
| SAMEA5767131 | smoking_status | current | R3 | 0.80 | paper.body.Table 1[Smoking] | Current |
Sequencing
9 runs over 9 samples · mean 9.68 Gbp per run (median 9.51 Gbp, total 87.10 Gbp; 9 runs with a base count) · layout PAIRED 9 · platform ILLUMINA 9 · models Illumina HiSeq 4000 (9) · 67% of runs with a Sandpiper profile · first public 2019-08-26
Authors (33)
Mas-Lloret J first · Obón-Santacana M · Ibáñez-Sanz G · Guinó E · Pato ML · Rodriguez-Moranta F · Mata A · García-Rodríguez A · Moreno V · Pimenoff VN last · Khan J first · Kokot M · Deorowicz S · Patro R last · Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last · Cracco A first · Tomescu AI last · De Biase R · Bocchio F · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R
Downloads
PRJEB33098.csv.gz (1.2 KB) · parquet (70.8 KB) — all 9 samples, every field with route and confidence · PRJEB33098_determinations.csv.gz (1.4 KB) — 98 evidence rows