Fecal metagenomes, B12 intake, healthy US adults, Davis CA
40 fecal metagenome samples from healthy adults in Davis, California, part of the USDA Nutritional Phenotyping Study, examining associations between dietary vitamin B12 intake and the gut microbiome in a cross-sectional design. machine-written summary
40 samples · 40 runs · US · Adult · 2024 · 15.43 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 239 sample values (collection date, country, latitude, location locality, location region, longitude) |
| ✓ Abstract / description | 80 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC11600052, PMC13502008 |
| ○ 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 |
Genera, mean relative abundance over 33 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 | 40 | 100% | ||||
| country | 40 | 100% | 40 | |||
| health_condition | 40 | 100% | 40 | |||
| subject_id | 0 | 0% | ||||
| detailed_location | 40 | 100% | ||||
| health_condition_detail | 40 | 100% | 40 | |||
| latitude | 40 | 100% | 40 | |||
| location_locality | 40 | 100% | 40 | |||
| location_region | 40 | 100% | 40 | |||
| longitude | 40 | 100% | 40 | |||
| collection_date | 39 | 98% | 39 |
- Diet, Microbiome, and Inflammation Predictors of Fecal and Plasma Short-Chain Fatty Acids in Humans. 2024 PMID 39173973 PMC11600052 unsure
- High dietary B<sub>12</sub> is associated with reduced gut microbial B<sub>12</sub> biosynthesis capacity and lower fecal short-chain fatty acids in healthy United States adults. 2026 PMID 42625439 PMC13502008 unsure
Archive description
Additional sequencing of stool metagenomes from the USDA's Nutritional Phenotyping Study (ClinicalTrials.gov ID: NCT02367287). Previous sequencing of 290 individuals are attached to the BioProject PRJNA795985.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.80. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “fecal samples from healthy US adults”
- life stage study.title · “healthy US adults”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN40576396 | collection_date | 2015-08-04 | R1 | 0.90 | biosample.attribute:collection_date | 2015-08-04 |
| SAMN40576396 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Davis, California |
| SAMN40576396 | health_condition | healthy_control | R4 | 0.50 | paper.abstract | healthy U.S. adults |
| SAMN40576396 | health_condition_detail | healthy U.S. adults | R4 | 0.50 | paper.abstract | healthy U.S. adults |
| SAMN40576396 | latitude | 38.5350 | R1 | 0.90 | biosample.attribute:lat_lon | 38.535039 N 121.766620 W |
| SAMN40576396 | location_locality | Davis | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Davis, California |
| SAMN40576396 | location_region | California | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Davis, California |
| SAMN40576396 | longitude | -121.7666 | R1 | 0.90 | biosample.attribute:lat_lon | 38.535039 N 121.766620 W |
Sequencing
40 runs over 40 samples · mean 15.66 Gbp per run (median 15.43 Gbp, total 626.55 Gbp; 40 runs with a base count) · layout PAIRED 40 · platform ILLUMINA 40 · models Illumina NovaSeq 6000 (40) · 82% of runs with a Sandpiper profile · first public 2024-09-29
Authors (13)
Oliver A first · Alkan Z · Stephensen CB · Newman JW · Kable ME · Lemay DG last · Hilliard MA first · Wilson SMG · Shahab-Ferdows S · Hampel D · Bennett BJ · Allen LH · G Lemay D last
Downloads
PRJNA1090850.csv.gz (2.1 KB) · parquet (71.5 KB) — all 40 samples, every field with route and confidence · PRJNA1090850_determinations.csv.gz (2.5 KB) — 319 evidence rows