Beef consumption diet trial for ARG transmission risk
226 fecal and beef samples from a randomized, controlled, crossover dietary intervention trial investigating transmission of antimicrobial resistance genes to consumers through beef consumption. machine-written summary
162 samples · 226 runs · US · Age unknown · 2026 · 9.23 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 806 sample values (collection date, country, location region, subject id, timepoint) |
| – Abstract / description | no abstract or project description |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 |
intervention — arms not resolved
Controlled / prescribed diet or feeding regimen design crossover · population healthy_control · Randomized crossover beef consumption dietary trial
“randomized, controlled, crossover dietary trial” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
26 of 26 people sampled more than once (160 samples; median 7, up to 7 per person) · follow-up median 3 mo (max 4 mo) · median interval between samples 14 d (time from collection dates). Schedule stated by the source: “Repeated fecal sampling across 7 timepoints (A-G) per subject in a crossover dietary intervention trial.”.
Each row is one person (26 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 158 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 | 162 | 100% | 162 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 160 | 99% | 160 | |||
| collection_date | 162 | 100% | 162 | |||
| detailed_location | 162 | 100% | ||||
| location_region | 162 | 100% | 162 | |||
| timepoint_label | 160 | 99% | 160 |
Archive description
Metagenomic sequencing samples from a randomized, controlled, crossover dietary trial to investigate the risk of transmitting antimicrobial resistance genes (ARG) to consumers through beef consumption.
How this project entered the registry
Classified as human and non-human (mixed) gut / stool / other human site shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.50. Assay shotgun_dna.
- host study.title · “Metagenomic sequencing of fecal and beef samples”
- body site study.title · “fecal and beef samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN54950209 | collection_date | 2021-03-08 | R1 | 0.90 | biosample.attribute:collection_date | 2021-03-08 |
| SAMN54950209 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Indiana |
| SAMN54950209 | location_region | Indiana | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Indiana |
| SAMN54950209 | subject_id | 101 | R1 | 0.70 | sample.name_rule:source_material_id | 101A |
| SAMN54950209 | timepoint_label | A | R1 | 0.70 | sample.name_rule:source_material_id | 101A |
Sequencing
226 runs over 162 samples · mean 10.92 Gbp per run (median 9.23 Gbp, total 2,468.61 Gbp; 226 runs with a base count) · layout PAIRED 226 · platform ILLUMINA 226 · models Illumina NovaSeq X Plus (226) · 75% of runs with a Sandpiper profile · first public 2026-02-07
Authors (0)
No author record.
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJNA1372133.csv.gz (5.5 KB) · parquet (76.1 KB) — all 162 samples, every field with route and confidence · PRJNA1372133_determinations.csv.gz (7.2 KB) — 806 evidence rows