Daily diet and gut microbiome in healthy US adults, 17 days
596 fecal metagenome samples from 34 healthy human subjects in the USA, collected daily over 17 days alongside 24-hour food records, in a longitudinal diet-intervention design. machine-written summary
596 samples · 596 runs · US · Age unknown · 2019 · 33.2 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3,576 sample values (collection date, country, health condition, health condition detail, latitude, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10292843, PMC8326577 |
| ✓ Supplementary tables | 596 sample values (subject id) |
| – 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 · Daily 24-hr food records; 2 subjects given monotonous meal-replacement beverage diet
“two subjects consuming only meal replacement beverages” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
37 of 37 people sampled more than once (596 samples; median 18, up to 23 per person). Schedule stated by the source: “fecal shotgun metagenomes collected daily over 17 days from the same subjects” (time origin: enrolment); stated follow-up 17 d.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 596 | 100% | 596 | |||
| health_condition | 596 | 100% | 596 | |||
| subject_id | 596 | 100% | 596 | |||
| collection_date | 596 | 100% | 596 | |||
| health_condition_detail | 596 | 100% | 596 | |||
| latitude | 596 | 100% | 596 | |||
| longitude | 596 | 100% | 596 |
- Universal gut microbial relationships in the gut microbiome of wild baboons. 2023 PMID 37158607 PMC10292843 own_data
- Linking Inflammatory Bowel Disease Symptoms to Changes in the Gut Microbiome Structure and Function. 2021 PMID 34349736 PMC8326577 unsure
Archive description
Diet is a key determinant of human gut microbiome variation. However, the fine-scale relationships between daily food choices and human gut microbiome composition remains unexplored. Here, we used multivariate methods to integrate 24-hour food records and fecal shotgun metagenomes from 34 healthy human subjects collected daily over 17 days. Microbiome composition depended on multiple days of dietary history and was more strongly associated with food choices than with conventional nutrient profiles, and daily microbial responses to diet were highly personalized. Data from two subjects consuming only meal replacement beverages suggests that a monotonous diet does not induce microbiome stability in humans, and instead overall dietary diversity associates with microbiome stability. Our work provides key methodological insights for future diet-microbiome studies and suggests that food-based interventions seeking to modulate the gut microbiota may need to be tailored to the individual microbiome.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.85. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- host study.description · “34 healthy human subjects”
- body site study.description · “fecal shotgun metagenomes”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA5604358 | collection_date | 2017-01-31 | R1 | 0.90 | biosample.attribute:collection_date | 2017-01-31 |
| SAMEA5604358 | country | US | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | USA |
| SAMEA5604358 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:DESCRIPTION | Healthy |
| SAMEA5604358 | health_condition_detail | Healthy | R1 | 0.85 | biosample.attribute:DESCRIPTION | Healthy |
| SAMEA5604358 | latitude | 44.9000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 44.9 N 93.2 W |
| SAMEA5604358 | longitude | -93.2000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 44.9 N 93.2 W |
| SAMEA5604358 | subject_id | MCTs01 | R2 | 0.75 | paper.repo.github.com/knights-lab/dietstudy_analyses:data/maps/SampleID_map.txt[UserName] | MCT.f.0001 UserName MCTs01 |
Sequencing
596 runs over 596 samples · mean 37.3 Mbp per run (median 33.2 Mbp, total 22.24 Gbp; 596 runs with a base count) · layout SINGLE 596 · platform ILLUMINA 596 · models Illumina HiSeq 2000 (526), Illumina MiSeq (70) · 0% of runs with a Sandpiper profile · first public 2019-05-11
Authors (17)
Hassouneh SA first · Loftus M · Yooseph S last · Roche KE first · Bjork JR · Dasari MR · Grieneisen L · Jansen D · Gould TJ · Gesquiere LR · Barreiro LB · Alberts SC · Blekhman R · Gilbert JA · Tung J · Mukherjee S · Archie EA last
Downloads
PRJEB29065.csv.gz (11.7 KB) · parquet (87.6 KB) — all 596 samples, every field with route and confidence · PRJEB29065_determinations.csv.gz (25.1 KB) — 4,172 evidence rows