Gut metagenomes for SCFA metabolic modeling, USA
36 gut metagenome samples from the USA, cross-sectional design, used to build community-scale metabolic models predicting individual short-chain-fatty-acid production profiles. machine-written summary
36 samples · 36 runs · US · Age unknown · 2023 · 0.37 Gbp / sample
One study deposited as 2 BioProjects (45 catalog samples together): PRJNA1033794 · PRJNA937304 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 336 sample values (collection date, country, intervention, latitude, location region, longitude, medication, medication detail) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 |
longitudinal — not resolved
2 of 2 people sampled more than once (36 samples; median 18, up to 18 per person). Schedule stated by the source: “Samples labeled by subject (Donor A/B), treatment (inulin/PBS/tryptophan), and timepoint (T0/T1); no explicit day/interval given”.
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 | 0 | 0% | ||||
| country | 36 | 100% | 36 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 36 | 100% | 36 | |||
| collection_date | 36 | 100% | 36 | |||
| detailed_location | 36 | 100% | ||||
| intervention | 36 | 100% | 36 | |||
| latitude | 36 | 100% | 36 | |||
| location_region | 36 | 100% | 36 | |||
| longitude | 36 | 100% | 36 | |||
| timepoint_label | 36 | 100% | 36 | |||
| medication | 24 | 67% | 24 | |||
| medication_detail | 24 | 67% | 24 |
- Microbial community-scale metabolic modelling predicts personalized short-chain fatty acid production profiles in the human gut. 2024 PMID 38914826 PMC11841136 unsure
Archive description
Microbially-derived short-chain fatty acids (SCFAs) in the human gut are tightly coupled to host metabolism, immune regulation, and integrity of the intestinal epithelium. However, the production of SCFAs can vary widely between individuals consuming the same diet, with lower levels often associated with disease. We lack a mechanistic understanding of this heterogeneity. We present a microbial community-scale metabolic modeling (MCMM) approach to predict individual-specific SCFA production profiles. We assess the quantitative accuracy of our MCMMs using in vitro, ex vivo, and in vivo data sets. Next, we identify associations between MCMM SCFA predictions and a panel of blood-based clinical chemistries in a large human cohort. Finally, we demonstrate how MCMMs can be leveraged to design personalized dietary, prebiotic, and probiotic interventions that optimize SCFA production in the gut. Our results represent an important advance in engineering gut microbiome functional outputs for precision health and nutrition.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.62. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.description · “short-chain fatty acids (SCFAs) in the human gut”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN33399093 | collection_date | 2019-10-18 | R1 | 0.90 | biosample.attribute:collection_date | 2019-10-18 |
| SAMN33399093 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN33399093 | intervention | placebo | R1 | 0.85 | biosample.attribute:treatment | PBS |
| SAMN33399093 | latitude | 42.3600 | R1 | 0.90 | biosample.attribute:lat_lon | 42.36 N 71.0941 W |
| SAMN33399093 | location_region | Massachusetts | R1 | 0.60 | biosample.attribute:lat_lon | 42.36 N 71.0941 W |
| SAMN33399093 | longitude | -71.0941 | R1 | 0.90 | biosample.attribute:lat_lon | 42.36 N 71.0941 W |
| SAMN33399099 | medication | other_medication | R1 | 0.75 | biosample.attribute:treatment | tryptophan |
| SAMN33399099 | medication_detail | tryptophan | R1 | 0.75 | biosample.attribute:treatment | tryptophan |
| SAMN33399093 | subject_id | Donor A | R1 | 0.85 | sample.attr.subject | Donor A |
| SAMN33399093 | timepoint_label | T0 | R1 | 0.85 | sample.attr.time_point | T0 |
Sequencing
36 runs over 36 samples · mean 0.37 Gbp per run (median 0.37 Gbp, total 13.47 Gbp; 36 runs with a base count) · layout SINGLE 36 · platform ILLUMINA 36 · models Illumina NovaSeq 6000 (36) · 92% of runs with a Sandpiper profile · first public 2023-11-01
Authors (11)
Quinn-Bohmann N first · Wilmanski T · Sarmiento KR · Levy L · Lampe JW · Gurry T · Rappaport N · Ostrem EM · Venturelli OS · Diener C · Gibbons SM last
Downloads
PRJNA937304.csv.gz (1.7 KB) · parquet (71.4 KB) — all 36 samples, every field with route and confidence · PRJNA937304_determinations.csv.gz (2.6 KB) — 336 evidence rows