Human gut virome and metagenome survey, China
298 fecal samples from Wuhan and Shanghai, China (adults and adolescents), analyzed via VLP-based virome sequencing (Illumina and PacBio) plus un-enriched metagenome sequencing, in a cross-sectional design. machine-written summary
298 samples · 381 runs · CN · Infant / toddler · 2024 · 15.52 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,036 sample values (age, bmi, collection date, country, diet, diet detail, health condition detail, latitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC12323601 |
| ○ 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
137 of 161 people sampled more than once (274 samples; median 2, up to 2 per person). Schedule stated by the source: “Not stated; described as cross-sectional, but each subject has up to 2 samples (median 2.0), likely corresponding to different sequencing modalities (vNGS/vTGS/mNGS) rather than separate timepoints.”.
Genera, mean relative abundance over 144 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 | 271 | 91% | ||||
| country | 298 | 100% | 298 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 298 | 100% | 298 | |||
| collection_date | 298 | 100% | 298 | |||
| age_at_collection_days | 271 | 91% | 271 | |||
| bmi | 271 | 91% | 258 | |||
| health_condition_detail | 271 | 91% | 258 | |||
| sex | 271 | 91% | 271 | |||
| detailed_location | 14 | 5% | ||||
| diet | 14 | 5% | 14 | |||
| diet_detail | 14 | 5% | 14 | |||
| latitude | 14 | 5% | 14 | |||
| location_locality | 14 | 5% | 14 | |||
| location_region | 14 | 5% | 14 | |||
| longitude | 14 | 5% | 14 |
- Biases and complementarity in gut viromes obtained from bulk and virus-like particle-enriched metagenomic sequencing. PMID 40600714 PMC12323601 curated
Archive description
To provide an unbiased survey of the human gut virome, we performed an amplification-independent analysis on fecal VLPs using NGS (Illumina) sequencing(vNGS) and TGS(Pacbio) sequencing(vTGS). This project also includes un-enriched metagenome sequencing(mNGS).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “Human feces Viral/Bacterial Metagenome”
- body site study.description · “of the human gut virome, we performed”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN28109061 | age_at_collection_days | 9131 | R1 | 0.90 | sample.attr.host_age | 25 |
| SAMN28109061 | bmi | 21.09 | R1 | 0.90 | biosample.attribute:host_body_mass_index | host_body_mass_index: 21.0938 |
| SAMN28109061 | collection_date | 2019-12-01 | R1 | 0.85 | biosample.attribute:collection_date | 2019-12-01 |
| SAMN28109061 | country | CN | R1 | 0.90 | biosample_attr | China: Wuhan |
| SAMN28109094 | diet | omnivore | R1 | 0.70 | biosample.attribute:host_diet | Normal diet |
| SAMN28109094 | diet_detail | Normal diet | R1 | 0.70 | biosample.attribute:host_diet | Normal diet |
| SAMN28109061 | health_condition_detail | No | R1 | 0.90 | biosample.attribute:liver_disord | liver_disord: No |
| SAMN28109202 | health_condition_detail | No | R1 | 0.90 | biosample.attribute:gastrointestinal_tract_disorder | gastrointestinal_tract_disorder: No |
| SAMN28109094 | latitude | 30.5200 | R1 | 0.90 | biosample.attribute:lat_lon | 30.52 N 114.42 E |
| SAMN28109094 | location_locality | Wuhan | R1 | 0.85 | biosample.attribute:geo_loc_name | China: Wuhan |
| SAMN28109094 | location_region | Hubei | R1 | 0.60 | biosample.attribute:lat_lon | 30.52 N 114.42 E |
| SAMN28109094 | longitude | 114.4200 | R1 | 0.90 | biosample.attribute:lat_lon | 30.52 N 114.42 E |
| SAMN28109061 | sex | female | R1 | 0.90 | biosample_attr | female |
| SAMN28109061 | subject_id | A01 | R1 | 0.70 | sample.name_rule:library_name | T-vA01;vA01 |
Sequencing
381 runs over 298 samples · mean 12.84 Gbp per run (median 11.71 Gbp, total 4,891.88 Gbp; 381 runs with a base count) · layout PAIRED 284, SINGLE 97 · platform DNBSEQ 142, ILLUMINA 142, PACBIO_SMRT 97 · models DNBSEQ-T7 (142), Illumina NovaSeq 6000 (142), Sequel II (97) · 34% of runs with a Sandpiper profile · first public 2024-05-26
Downloads
PRJNA835720.csv.gz (10.4 KB) · parquet (85.7 KB) — all 298 samples, every field with route and confidence · PRJNA835720_determinations.csv.gz (18.9 KB) — 2,036 evidence rows