Gut metagenome of healthy US adults, Davis CA, diet and AMR
Shotgun metagenome sequencing of 290 fecal samples from healthy adults in Davis, California, in a cross-sectional study examining associations between dietary intake (including monosaccharide composition) and gut antimicrobial resistance genes. machine-written summary
290 samples · 290 runs · US · Adult · 2022 · 9.29 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,740 sample values (collection date, country, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 290 sample values (subject id) · PMC10196574, PMC11600052, PMC12838403, PMC9239165 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 580 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 269 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 | 290 | 100% | ||||
| country | 290 | 100% | 290 | |||
| health_condition | 290 | 100% | 290 | |||
| subject_id | 290 | 100% | 290 | |||
| collection_date | 290 | 100% | 290 | |||
| detailed_location | 290 | 100% | ||||
| health_condition_detail | 290 | 100% | 290 | |||
| latitude | 290 | 100% | 290 | |||
| location_locality | 290 | 100% | 290 | |||
| location_region | 290 | 100% | 290 | |||
| longitude | 290 | 100% | 290 |
- Association of Diet and Antimicrobial Resistance in Healthy U.S. Adults. 2022 PMID 35536006 PMC9239165 own_data
- Dietary Intake of Monosaccharides from Foods is Associated with Characteristics of the Gut Microbiota and Gastrointestinal Inflammation in Healthy US Adults. 2023 PMID 36913444 PMC10196574 own_data
- Molecular evolution and diversity of isomerase-reductase clusters involved in the bacterial metabolism of glycosaminoglycans. 2026 PMID 41459968 PMC12838403 own_data
- 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
Antimicrobial resistance (AMR) represents a significant source of morbidity and mortality worldwide, with expectations that AMR-associated consequences will continue to worsen throughout the coming decades. Since resistance to antibiotics is encoded in the microbiome, interventions aimed at altering the taxonomic composition of the gut might allow us to prophylactically engineer microbiomes that harbor less AMR. Diet is one method of intervention, yet little is known about the association between diet and antimicrobial resistance. We sequenced the microbial DNA in 290 individuals' guts and examined the relationship between genes that confer antimicrobial resistance with the individuals' diets.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.85. 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 |
|---|---|---|---|---|---|---|
| SAMN24806631 | collection_date | 2015-06-01 | R1 | 0.90 | biosample.attribute:collection_date | 2015-06-01 |
| SAMN24806631 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Davis, California |
| SAMN24806631 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN24806631 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN24806631 | latitude | 38.5350 | R1 | 0.90 | biosample.attribute:lat_lon | 38.535039 N 121.766620 W |
| SAMN24806631 | location_locality | Davis | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Davis, California |
| SAMN24806631 | location_region | California | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Davis, California |
| SAMN24806631 | longitude | -121.7666 | R1 | 0.90 | biosample.attribute:lat_lon | 38.535039 N 121.766620 W |
| SAMN24806631 | subject_id | SAMN24806631 | R3 | 0.75 | design.one_sample_per_subject:fulltext | Participants were instructed to collect a single stool sample in a Ziploc bag |
Sequencing
290 runs over 290 samples · mean 9.33 Gbp per run (median 9.29 Gbp, total 2,704.67 Gbp; 290 runs with a base count) · layout PAIRED 290 · platform ILLUMINA 290 · models Illumina NovaSeq 6000 (290) · 93% of runs with a Sandpiper profile · first public 2022-04-26
Authors (32)
Oliver A first · Xue Z · Villanueva YT · Durbin-Johnson B · Alkan Z · Taft DH · Liu J · Korf I · Laugero KD · Stephensen CB · Mills DA · Kable ME · Lemay DG last · Larke JA first · Bacalzo N · Castillo JJ · Couture G · Chen Y · Lebrilla CB · Newman JW · Nishimura Y first · Okumura K · Oiki S · Ogura K · Hashimoto W last · Hilliard MA first · Wilson SMG · Shahab-Ferdows S · Hampel D · Bennett BJ · Allen LH · G Lemay D last
Downloads
PRJNA795985.csv.gz (9.1 KB) · parquet (84.1 KB) — all 290 samples, every field with route and confidence · PRJNA795985_determinations.csv.gz (18.7 KB) — 2,610 evidence rows