Fecal virome method comparison in Lynch syndrome adults, Spain
72 stool samples from adult Lynch syndrome mutation carriers in Spain, cross-sectional design, comparing bulk-metagenome versus virus-like particle enrichment protocols for virome characterization. machine-written summary
72 samples · 72 runs · ES · Adult · 2024 · 0.33 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 348 sample values (collection date, country, latitude, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 288 sample values (health condition, health condition detail, location region, location site) · PMC10820677 |
| ○ 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 |
longitudinal — not resolved
10 of 10 people sampled more than once (60 samples; median 6, up to 6 per person).
Genera, mean relative abundance over 1 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 | 72 | 100% | ||||
| country | 72 | 100% | 72 | |||
| health_condition | 72 | 100% | 72 | |||
| subject_id | 60 | 83% | 60 | |||
| collection_date | 72 | 100% | 72 | |||
| detailed_location | 72 | 100% | ||||
| health_condition_detail | 72 | 100% | 72 | |||
| latitude | 72 | 100% | 72 | |||
| location_region | 72 | 100% | 72 | |||
| location_site | 72 | 100% | 72 | |||
| longitude | 72 | 100% | 72 |
- Comparison of Experimental Methodologies Based on Bulk-Metagenome and Virus-like Particle Enrichment: Pros and Cons for Representativeness and Reproducibility in the Study of the Fecal Human Virome. 2024 PMID 38257988 PMC10820677 own_data
Archive description
Retrospective study to characterize the fecal virome for comparison of viral metagenomics approaches. Stool samples from 10 healthy adults, carriers of Lynch syndrome mutations were collected, and the virome was extracted following three protocols: Protocol 1, based on based on bulk metagenomics, and 2 and 3, based on virus-like particle (VLP) enrichment, with two replicas per protocol. Negative controls of extraction, retrotranscription and amplification were run in parallel to samples Libraries were sequenced on the Illumina NextSeq 500 producing 1x150 bp single-end reads. The resulting single-end reads were filtered for quality and taxa were assigned using Kaiju. Alpha diversity was analyzed by Shannon index and beta diversity by Bray-Curtis dissimilarity.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.description · “Stool samples from 10 healthy adults”
- life stage study.description · “Stool samples from 10 healthy adults”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA114770520 | collection_date | 2021 | R1 | 0.90 | biosample.attribute:collection_date | 2021 |
| SAMEA114770520 | country | ES | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Spain |
| SAMEA114770520 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | cohort of healthy volunteers from the Valencian Region |
| SAMEA114770520 | health_condition_detail | healthy volunteers, carriers of Lynch syndrome mutations | R3 | 0.70 | paper.fulltext.methods | cohort of healthy volunteers from the Valencian Region |
| SAMEA114770520 | latitude | 39.4767 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 39.476667 0.374444 |
| SAMEA114770520 | location_region | Valencian Region | R3 | 0.60 | paper.fulltext.results | ten volunteers recruited in the Valencian Region |
| SAMEA114770520 | location_site | Program of Genetic Counseling in Cancer of the Valencian Community | R3 | 0.70 | paper.fulltext.methods | Program of Genetic Counseling in Cancer of the Valencian Community |
| SAMEA114770520 | longitude | 0.3744 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 39.476667 0.374444 |
| SAMEA114770520 | subject_id | ML002 | R1 | 0.70 | sample.name_rule:alias | ML002_T09_1A |
Sequencing
72 runs over 72 samples · mean 0.35 Gbp per run (median 0.33 Gbp, total 24.93 Gbp; 72 runs with a base count) · layout SINGLE 72 · platform ILLUMINA 72 · models NextSeq 500 (72) · 1% of runs with a Sandpiper profile · first public 2024-01-14
Authors (6)
Soria-Villalba A first · Pesantes N · Jiménez-Hernández N · Pons J · Moya A · Pérez-Brocal V last
Downloads
PRJEB70723.csv.gz (2.7 KB) · parquet (73.8 KB) — all 72 samples, every field with route and confidence · PRJEB70723_determinations.csv.gz (4.6 KB) — 636 evidence rows