AMY1 copy number and gut microbiome diet intervention, USA
140 stool samples from adults in the USA, studying how salivary amylase (AMY1) gene copy number relates to gut microbiome composition and function during a standardized diet intervention. machine-written summary
140 samples · 597 runs · US · Adult · 2019 · 15.21 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,400 sample values (age, bmi, collection date, country, latitude, location region, longitude, sex) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10688793, PMC13106387 |
| ○ 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 |
intervention — arms not resolved
Controlled / prescribed diet or feeding regimen design single_arm_before_after · population healthy_control · 2-week standard diet to assess AMY1 copy-number effects
“2-week standard diet” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
25 of 25 people sampled more than once (140 samples; median 6, up to 6 per person).
Genera, mean relative abundance over 138 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 | 140 | 100% | ||||
| country | 140 | 100% | 140 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 140 | 100% | 140 | |||
| age_at_collection_days | 140 | 100% | 140 | |||
| bmi | 140 | 100% | 140 | |||
| collection_date | 140 | 100% | 140 | |||
| detailed_location | 140 | 100% | ||||
| latitude | 140 | 100% | 140 | |||
| location_region | 140 | 100% | 140 | |||
| longitude | 140 | 100% | 140 | |||
| sex | 140 | 100% | 140 | |||
| timepoint_label | 140 | 100% | 140 |
- Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes. 2019 PMID 30974084 own_data
- Profiling of the intestinal community of Clostridia: taxonomy and evolutionary analysis. 2023 PMID 38047279 PMC10688793 unsure
- A genomic atlas of gut clostridia: phylogeny, butyrate, and propionate production. 2026 PMID 42039832 PMC13106387 unsure
Archive description
Human genetic variation influences the composition of the gut microbiome. Studies have focused on associations between components of the microbiome and single nucleotide polymorphisms in genes, but their copy number (CN) can also vary. Here, we relate oral and gut microbiome to CN variation at the AMY1 locus, encoding the salivary amylase gene active in starch degradation, in a study of human subjects including a 2-week standard diet. We show that diet standardization drove gut microbiome convergence, yet AMY1-CN influenced oral and gut microbiome composition and function. Low-AMY1-subject gut microbiomes showed an enhanced capacity for breakdown of complex carbohydrates, and high-AMY1 an enrichment of microbiota linked to resistant starch fermentation. High-AMY1-subject microbiomes were associated with higher fecal SCFAs, and drove higher adiposity when transferred to germfree mice. This study establishes AMY1-CN as a significant genetic factor patterning microbiome composition and function, with implications for personalized nutrition targeting microbiomes.
How this project entered the registry
Classified as human gut / stool / oral cavity shotgun DNA metagenome of adult and adolescent by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host run.scientific_name · “human metagenome”
- body site study.description · “relate oral and gut microbiome”
- life stage sample.attr.age · “20 (n=122/140)”
- life stage sample.attr.age · “19 (n=18/140)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA4731419 | age_at_collection_days | 9496.5 | R1 | 0.85 | sample.attr.age | 26 |
| SAMEA4731419 | bmi | 24.05 | R1 | 0.90 | sample.attr.bmi | 24.04764987 |
| SAMEA4731419 | collection_date | 2010-01-01 | R1 | 0.90 | biosample.attribute:collection_date | 2010-01-01 |
| SAMEA4731419 | country | US | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | USA |
| SAMEA4731419 | latitude | 42.4485 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 42.44851 -76.47862 |
| SAMEA4731419 | location_region | New York | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 42.44851 -76.47862 |
| SAMEA4731419 | longitude | -76.4786 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 42.44851 -76.47862 |
| SAMEA4731419 | sex | female | R1 | 0.90 | sample.attr.gender | female |
| SAMEA4731419 | subject_id | 2 | R1 | 0.85 | sample.attr.subjectid | 2 |
| SAMEA4731419 | timepoint_label | 7 | R1 | 0.85 | sample.attr.timepoint | 7 |
Sequencing
597 runs over 140 samples · mean 3.45 Gbp per run (median 3.40 Gbp, total 2,057.31 Gbp; 597 runs with a base count) · layout PAIRED 597 · platform ILLUMINA 597 · models Illumina HiSeq 3000 (597) · 89% of runs with a Sandpiper profile · first public 2019-04-15
Authors (21)
Poole AC first · Goodrich JK · Youngblut ND · Luque GG · Ruaud A · Sutter JL · Waters JL · Shi Q · El-Hadidi M · Johnson LM · Bar HY · Huson DH · Booth JG · Ley RE last · Candeliere F first · Musmeci E · Amaretti A · Sola L · Raimondi S · Rossi M last · Busi E
Downloads
PRJEB27308.csv.gz (4.5 KB) · parquet (75.8 KB) — all 140 samples, every field with route and confidence · PRJEB27308_determinations.csv.gz (9.8 KB) — 1,400 evidence rows