Gut microbiome and transit time in UK/USA adults (PREDICT 1)
1098 gut metagenome samples from healthy adults in the UK (1001) and USA (97), studying links between gut transit time (blue dye method), microbiome composition, cardiometabolic markers and diet; single-arm intervention study. machine-written summary
1,098 samples · 1,098 runs · GB, US · Age unknown · 2020 · 8.10 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 5,490 sample values (collection date, country, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10140478, PMC10395212, PMC10549191, PMC10609127, PMC10810176, PMC11304618, PMC11322291, PMC11602726, PMC11726441, PMC12678775, PMC12960697, PMC13079874, PMC8349893, PMC8353542, PMC9469561, PMC9805558 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 6,587 sample values (age, antibiotic exposure, bmi, health condition, health condition detail, sex) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Other administered intervention (see intervention_detail) design observational_with_procedure · population healthy_control · Standardised test meals for postprandial metabolic response assessment
“PREDICT 1 metagenomic study” — study.title (study level; per-sample arms are in the intervention column below)
twins — not resolved
PREDICT 1: UK twins plus unrelated adults (UK, USA); twin-pair ids not in the archive, no per-sample rows.
Genera, mean relative abundance over 981 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 | 1,076 | 98% | ||||
| country | 1,098 | 100% | 1,098 | |||
| health_condition | 1,098 | 100% | 1,098 | |||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 1,098 | 100% | 1,098 | |||
| antibiotic_exposure | 1,098 | 100% | 1,098 | |||
| collection_date | 1,098 | 100% | 1,098 | |||
| detailed_location | 1,098 | 100% | ||||
| health_condition_detail | 1,098 | 100% | 1,098 | |||
| latitude | 1,098 | 100% | 1,098 | |||
| location_region | 1,098 | 100% | 1,098 | |||
| longitude | 1,098 | 100% | 1,098 | |||
| sex | 1,098 | 100% | 1,098 | |||
| bmi | 1,097 | 100% | 1,097 |
- Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals. 2021 PMID 33432175 PMC8353542 own_data
- Blue poo: impact of gut transit time on the gut microbiome using a novel marker. 2021 PMID 33722860 PMC8349893 own_data
- Diet and gut microbial associations in irritable bowel syndrome according to disease subtype. 2023 PMID 37786251 PMC10549191 own_data
- Insights into the ecology of the infant gut plasmidome. 2024 PMID 39138199 PMC11322291 own_data
- Metagenomics indicates an interplay of the microbiome and functional pathways in Parkinson's disease. 2026 PMID 41618101 PMC12960697 own_data
13 more
- Metagenomics Indicates an Interplay of the Microbiome and Functional Pathways in Parkinson's Disease 2025
- Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population. 2022 PMID 36100953 PMC9469561
- MIDAS2: Metagenomic Intra-species Diversity Analysis System. 2023 PMID 36321886 PMC9805558
- The secondary bile acid isoursodeoxycholate correlates with post-prandial lipemia, inflammation, and appetite and changes post-bariatric surgery. 2023 PMID 37023745 PMC10140478
- Toward an improved definition of a healthy microbiome for healthy aging. 2022 PMID 37118093 PMC10154212
- Genetic and gut microbiome determinants of SCFA circulating and fecal levels, postprandial responses and links to chronic and acute inflammation. 2023 PMID 37526398 PMC10395212
- A Pipeline for Constructing Reference Genomes for Large Cohort-Specific Metagenome Compression. 2023 PMID 37894218 PMC10609127
- Meta-analysis reveals obesity associated gut microbial alteration patterns and reproducible contributors of functional shift. 2024 PMID 38265338 PMC10810176
- Vitamin A carotenoids, but not retinoids, mediate the impact of a healthy diet on gut microbial diversity. 2024 PMID 39113058 PMC11304618
- Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts. 2024 PMID 39558133 PMC11602726
- Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals. 2025 PMID 39762435 PMC11726441
- Faecal metabolites as a readout of habitual diet capture dietary interactions with the gut microbiome. 2025 PMID 41345102 PMC12678775
- Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery. 2026 PMID 41980943 PMC13079874
Archive description
Study aimed to find associations between microbiome composition and habitual diet, cardiometabolic markers, and postprandial blood markers
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.60. Assay shotgun_dna.
- host study.description · “habitual diet, cardiometabolic markers, and postprandial blood markers”
- body site sample.attr.environment_biome · “human-gut (n=1098/1098)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA7041133 | age_at_collection_days | 13149.0 | R2 | 0.75 | external.cmd source | age: 36; age_unit: Year; age_group: Adult |
| SAMEA7041133 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMEA7041133 | bmi | 37.27 | R2 | 0.75 | external.cmd source | bmi: 37.2684927568031 |
| SAMEA7041133 | collection_date | 2019 | R1 | 0.90 | biosample.attribute:collection_date | 2019 |
| SAMEA7041133 | country | US | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | USA |
| SAMEA7041133 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMEA7041133 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMEA7041133 | latitude | 42.3611 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 42.361145 -71.057083 |
| SAMEA7041133 | location_region | Massachusetts | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 42.361145 -71.057083 |
| SAMEA7041133 | longitude | -71.0571 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 42.361145 -71.057083 |
| SAMEA7041133 | sex | female | R2 | 0.75 | external.cmd source | sex: Female |
Sequencing
1,098 runs over 1,098 samples · mean 8.76 Gbp per run (median 8.10 Gbp, total 9,620.68 Gbp; 1,098 runs with a base count) · layout PAIRED 1,098 · platform ILLUMINA 1,098 · models Illumina NovaSeq 6000 (1,098) · 89% of runs with a Sandpiper profile · first public 2020-08-10
Authors (60)
Zhao C first · Dimitrov B · Goldman M · Nayfach S · Pollard KS last · He W first · Russel J · Klincke F · Nesme J · Sørensen SJ last · Nooij S first · Plomp N · Sanders IMJG · Schout L · van der Meulen AE · Terveer EM · Norman JM · Karcher N · Larralde MF · Vossen RHAM · Kloet SL · Faber KN · Harmsen HJM · Zeller GF · Kuijper EJ · Smits WK · Ducarmon QR last · Pope R first · Visconti A · Zhang X · Louca P · Baleanu AF · Lin Y · Asnicar F · Bermingham K · Wong KE · Michelotti GA · Wolf J · Segata N · Berry SE · Spector TD · Leeming ER · Gibson R · Menni C · Falchi M last · Park SJ first · Özdinç BE · Coker KG · Walsh DM · Fox DJ · Evans S · Farahnik J · Moffat K · Boomgaarden M · Mischley LK last · Kim J first · Kim N · Cha JH · Ma J · Lee I last
Downloads
PRJEB39223.csv.gz (32.9 KB) · parquet (117.5 KB) — all 1,098 samples, every field with route and confidence · PRJEB39223_determinations.csv.gz (120.5 KB) — 12,077 evidence rows