Long-read phage dynamics in healthy US gut microbiomes
12 stool samples from six healthy adult volunteers in the USA, collected two years apart, analyzed by long-read metagenomics to track prophage gain/loss and induction dynamics in a longitudinal design. machine-written summary
12 samples · 24 runs · US · Adult · 2025 · 36.29 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 84 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 12 sample values (health condition) |
| ○ Full text | read; no usable statement or table · PMC12823448 |
| ○ 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
6 of 6 people sampled more than once (12 samples; median 2, up to 2 per person) · follow-up median 2.0 y (max 2.0 y) · median interval between samples 2.0 y (time from visit codes mapped to the stated schedule). Schedule stated by the source: “stool samples from same six volunteers, sampled two years apart” (time origin: baseline); stated follow-up 2.0 y.
Each row is one person (6 shown); dots are samples at days since that person's first sample.
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 | 12 | 100% | ||||
| country | 12 | 100% | 12 | |||
| health_condition | 12 | 100% | 12 | |||
| subject_id | 12 | 100% | 12 | |||
| collection_date | 12 | 100% | 12 | |||
| detailed_location | 12 | 100% | ||||
| latitude | 12 | 100% | 12 | |||
| location_region | 12 | 100% | 12 | |||
| longitude | 12 | 100% | 12 | |||
| timepoint_label | 12 | 100% | 12 |
- Long-read metagenomics reveals phage dynamics in the human gut microbiome. 2026 PMID 41299176 PMC12823448 unsure
Archive description
These data derive from stool metagenomic sequencing of six healthy volunteers, sampled two years apart.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.description · “stool metagenomic sequencing of six healthy volunteers”
- life stage study.description · “six healthy volunteers, sampled two years apart”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA117989187 | collection_date | 2021/2023 | R1 | 0.90 | biosample.attribute:collection_date | 2021/2023 |
| SAMEA117989187 | country | US | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | USA |
| SAMEA117989187 | health_condition | healthy_control | R4 | 0.50 | study.description | six healthy volunteers |
| SAMEA117989187 | latitude | 37.4308 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 37.430774 -122.169213 |
| SAMEA117989187 | location_region | California | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 37.430774 -122.169213 |
| SAMEA117989187 | longitude | -122.1692 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 37.430774 -122.169213 |
| SAMEA117989187 | subject_id | D02 | R1 | 0.70 | sample.name_rule:TITLE | D02_T1 |
| SAMEA117989187 | timepoint_label | T1 | R1 | 0.70 | sample.name_rule:TITLE | D02_T1 |
Sequencing
24 runs over 12 samples · mean 17.93 Gbp per run (median 11.69 Gbp, total 430.35 Gbp; 24 runs with a base count) · layout SINGLE 18, PAIRED 6 · platform ILLUMINA 12, OXFORD_NANOPORE 12 · models Illumina NovaSeq 6000 (12), PromethION (12) · 25% of runs with a Sandpiper profile · first public 2025-10-09
Authors (8)
Wirbel J first · Hickey AS · Chang D · Enright NJ · Dvorak M · Chanin RB · Schmidtke DT · Bhatt AS last
Downloads
PRJEB88320.csv.gz (1.2 KB) · parquet (70.3 KB) — all 12 samples, every field with route and confidence · PRJEB88320_determinations.csv.gz (1.3 KB) — 96 evidence rows