Dairy farmer, cow, and non-farmer nasal/gut microbiomes, WI
891 nasal and fecal samples from dairy farmers, dairy cows, and matched non-farmers in Marshfield, WI, in a longitudinal study of occupational farm-exposure effects on microbiome composition. machine-written summary
444 samples · 891 runs · US · Age unknown · 2024 · 4.16 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3,242 sample values (collection date, country, latitude, location locality, location region, longitude, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 444 sample values (location site) · PMC11966613 |
| – 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
86 of 117 people sampled more than once (254 samples; median 3, up to 5 per person) · follow-up median 6 mo (max 12 mo) · median interval between samples 3 mo (time from collection dates). Schedule stated by the source: “Multiple visit timepoints per subject (S001, V101-V401, P001, F001, W001) over a year-long period”; stated follow-up 12 mo.
Each row is one person (36 shown of 86); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 699 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 | 444 | 100% | ||||
| country | 444 | 100% | 444 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 293 | 66% | 293 | |||
| collection_date | 444 | 100% | 444 | |||
| detailed_location | 444 | 100% | ||||
| latitude | 444 | 100% | 444 | |||
| location_locality | 444 | 100% | 444 | |||
| location_region | 444 | 100% | 444 | |||
| location_site | 444 | 100% | 444 | |||
| longitude | 444 | 100% | 444 | |||
| timepoint_label | 285 | 64% | 285 |
- Longitudinal dynamics of farmer and livestock nasal and faecal microbiomes and resistomes. 2024 PMID 38570675 PMC11966613 own_data
Archive description
Profiling of the nasal and gut microbiomes of dairy cows, dairy farmers, and non-farmers to assess the occupational signatures of the farmer microbial communities.
How this project entered the registry
Classified as human and non-human (mixed) gut / stool / nasal / nasopharyngeal shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “upper respiratory tract metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN34495661 | collection_date | 2019-03-20 | R1 | 0.90 | biosample.attribute:collection_date | 2019-03-20 |
| SAMN34495661 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Marshfield, WI |
| SAMN34495661 | latitude | 44.6900 | R1 | 0.90 | biosample.attribute:lat_lon | 44.69 N 90.17 W |
| SAMN34495661 | location_locality | Marshfield | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Marshfield, WI |
| SAMN34495661 | location_region | Wisconsin | R1 | 0.75 | biosample.attribute:geo_loc_name | USA: Marshfield, WI |
| SAMN34495661 | location_site | Marshfield Clinic Health System | R3 | 0.70 | paper.fulltext.methods | Marshfield Clinic Health System (MCHS) Medical History Number |
| SAMN34495661 | longitude | -90.1700 | R1 | 0.90 | biosample.attribute:lat_lon | 44.69 N 90.17 W |
| SAMN34495661 | subject_id | W0102 | R1 | 0.85 | sample.attr.subject_id | W0102 |
| SAMN34495661 | timepoint_label | W001 | R1 | 0.70 | sample.name_rule:alias | 19-W0102-W001fc01 |
Sequencing
891 runs over 444 samples · mean 4.03 Gbp per run (median 4.16 Gbp, total 3,594.50 Gbp; 891 runs with a base count) · layout PAIRED 891 · platform ILLUMINA 891 · models Illumina NovaSeq 6000 (740), NextSeq 2000 (151) · 89% of runs with a Sandpiper profile · first public 2024-01-30
Authors (15)
Mahmud B first · Vargas RC · Sukhum KV · Patel S · Liao J · Hall LR · Kesaraju A · Le T · Kitchner T · Kronholm E · Koshalek K · Bendixsen CG · VanWormer JJ · Shukla SK · Dantas G last
Downloads
PRJNA964705.csv.gz (13.5 KB) · parquet (88.6 KB) — all 444 samples, every field with route and confidence · PRJNA964705_determinations.csv.gz (26.9 KB) — 3,686 evidence rows