Metagenome samples, California, sequencing method comparison
70 stool samples from ten donors in California, USA, preserved in different collection kits under a range of conditions to quantify sample-collection bias in relative and absolute microbiome measurements. machine-written summary
70 samples · 220 runs · US · Age unknown · 2023 · 33.58 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 480 sample values (collection date, country, intervention, latitude, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11836353, PMC11949080, PMC12363240 |
| ○ 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 · share metadata |
| – 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 (70 samples; median 7, up to 7 per person).
Genera, mean relative abundance over 70 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 | 0 | 0% | ||||
| country | 70 | 100% | 70 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 70 | 100% | 70 | |||
| collection_date | 70 | 100% | 70 | |||
| detailed_location | 70 | 100% | ||||
| latitude | 70 | 100% | 70 | |||
| location_region | 70 | 100% | 70 | |||
| longitude | 70 | 100% | 70 | |||
| intervention | 60 | 86% | 60 |
- Viroid-like colonists of human microbiomes. 2024 PMID 39481381 PMC11949080 own_data
- Illumina complete long read assay yields contiguous bacterial genomes from human gut metagenomes. 2025 PMID 40698936 PMC12363240 own_data
- Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo. 2025 PMID 39966439 PMC11836353 unsure
- Long-read metagenomics reveals phage dynamics in the human gut microbiome. 2026 PMID 41299176 PMC12823448 unsure
Archive description
These data represent metagenomic and metatranscriptomic analyses of human stool samples preserved in DNA Genotek OMR-200 collection kits and Zymo DNA/RNA Shield collection kits, after exposure to a range of collection conditions. Ten donors were analyzed, and collection conditions were replicated in triplicate.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “human stool samples preserved in”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN33571935 | collection_date | 2021 | R1 | 0.90 | biosample.attribute:collection_date | 2021 |
| SAMN33571935 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:California |
| SAMN33571935 | intervention | other_intervention | R1 | 0.85 | biosample.attribute:samp_collect_device | DNA Genotek OMR-200 |
| SAMN33571935 | latitude | 37.4300 | R1 | 0.90 | biosample.attribute:lat_lon | 37.43 N 122.17 W |
| SAMN33571935 | location_region | California | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:California |
| SAMN33571935 | longitude | -122.1700 | R1 | 0.90 | biosample.attribute:lat_lon | 37.43 N 122.17 W |
| SAMN33571935 | subject_id | D04 | R1 | 0.50 | sample.attr.donor | D04 |
Sequencing
220 runs over 70 samples · mean 11.30 Gbp per run (median 8.47 Gbp, total 2,485.07 Gbp; 220 runs with a base count) · layout PAIRED 210, SINGLE 10 · platform ILLUMINA 210, OXFORD_NANOPORE 10 · models Illumina NovaSeq 6000 (210), PromethION (10) · 87% of runs with a Sandpiper profile · first public 2023-03-17
Authors (30)
Zheludev IN first · Edgar RC · Lopez-Galiano MJ · de la Peña M · Babaian A · Bhatt AS · Fire AZ last · Chen X first · Yin X · Xu X · Zhang T last · Maghini DG first · Kiguchi Y · Darling AE · Monahan LG · Halpern AL · Burke CM · Jaeger E · Statham A · Truong T · Ying K · Bruinsma SP · Schroth GP · Wirbel J first · Hickey AS · Chang D · Enright NJ · Dvorak M · Chanin RB · Schmidtke DT
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJNA940499.csv.gz (2.6 KB) · parquet (72.4 KB) — all 70 samples, every field with route and confidence · PRJNA940499_determinations.csv.gz (3.3 KB) — 480 evidence rows