Storage buffer effects on human gut virome, Copenhagen
22 fecal samples from healthy adults in Copenhagen, Denmark, used to test how storage buffers, temperature, and time affect bacteriophage infectivity and metavirome sequencing composition, in an intervention study. machine-written summary
22 samples · 22 runs · DK · Age unknown · 2023 · 0.31 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 148 sample values (collection date, country, latitude, location locality, location region, longitude, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 44 sample values (health condition, health condition detail) · PMC10463696, PMC13473319 |
| ○ 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 |
intervention — arms not resolved
Other administered intervention (see intervention_detail) design single_arm_before_after · population healthy_control · Fecal samples spiked with phages (T4, c2, Phi X174), stored in buffers (SM, CANVAX, DNA/RNA Shield, StayRNA, RNAlater) at varying
“infectivity and genome recovery rate of different spiked bacteriophages” — abstract:37635262 (study level; per-sample arms are in the intervention column below)
Genera, mean relative abundance over 16 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 | 22 | 100% | ||||
| country | 22 | 100% | 22 | |||
| health_condition | 22 | 100% | 22 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 22 | 100% | 22 | |||
| detailed_location | 22 | 100% | ||||
| health_condition_detail | 22 | 100% | 22 | |||
| latitude | 22 | 100% | 22 | |||
| location_locality | 22 | 100% | 22 | |||
| location_region | 22 | 100% | 22 | |||
| longitude | 22 | 100% | 22 | |||
| timepoint_label | 16 | 73% | 16 |
- The impact of storage buffer and storage conditions on fecal samples for bacteriophage infectivity and metavirome analyses. 2023 PMID 37635262 PMC10463696 own_data
- metaIVP: an integrative metavirome focused metagenomic processing pipeline. 2026 PMID 42602060 PMC13473319 own_data
Archive description
This part of sequencing data is used for the investigation of the effects of storage conditions and storage buffers on the human gut virome
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “human gut virome”
- body site study.description · “human gut virome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN32874262 | collection_date | 2019-12 | R1 | 0.90 | biosample.attribute:collection_date | 2019-12 |
| SAMN32874262 | country | DK | R1 | 0.90 | sample.attr.geo_loc_name | Denmark: Copenhagen |
| SAMN32874262 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | donated by an anonymous healthy adult donor |
| SAMN32874262 | health_condition_detail | Healthy adult stool donor, spiked with bacteriophages for storage experiment | R3 | 0.70 | paper.fulltext.methods | donated by an anonymous healthy adult donor |
| SAMN32874262 | latitude | 55.6761 | R1 | 0.90 | biosample.attribute:lat_lon | 55.6761 N 12.5689 E |
| SAMN32874262 | location_locality | Copenhagen | R1 | 0.85 | biosample.attribute:geo_loc_name | Denmark: Copenhagen |
| SAMN32874262 | location_region | Capital Region | R1 | 0.60 | biosample.attribute:lat_lon | 55.6761 N 12.5689 E |
| SAMN32874262 | longitude | 12.5689 | R1 | 0.90 | biosample.attribute:lat_lon | 55.6761 N 12.5689 E |
| SAMN32874262 | timepoint_label | Day0 | R1 | 0.85 | biosample.attribute:storage_time | Day0 |
Sequencing
22 runs over 22 samples · mean 1.27 Gbp per run (median 0.31 Gbp, total 27.87 Gbp; 22 runs with a base count) · layout PAIRED 22 · platform ILLUMINA 22 · models NextSeq 550 (22) · 73% of runs with a Sandpiper profile · first public 2023-01-24 – 2023-01-25
Authors (9)
Zhai X first · Castro-Mejía JL · Gobbi A · Aslampaloglou A · Kot W · Nielsen DS · Deng L last · Sahu K first · Yao Q last
Downloads
PRJNA926386.csv.gz (1.5 KB) · parquet (71.1 KB) — all 22 samples, every field with route and confidence · PRJNA926386_determinations.csv.gz (1.9 KB) — 192 evidence rows