Dietary intervention in pre-diabetic adults, Israel
706 samples from a six-month dietary intervention trial in pre-diabetic adults in Israel, comparing a personalized postprandial glucose-targeting diet to a standard Mediterranean diet, with oral and gut microbiome, metabolite and cytokine profiling. machine-written summary
706 samples · 706 runs · IL · Adult · 2023 · 0.91 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,824 sample values (collection date, country, subject id, timepoint) |
| ✓ Abstract / description | 1,412 sample values (health condition, health condition detail) |
| ✓ Full text | 1,412 sample values (antibiotic exposure, location site) · PMC10477304, PMC5323868 |
| ✓ Supplementary tables | 702 sample values (intervention) |
| – 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 randomized_controlled_trial · population type2_diabetes · Six-month personalized postprandial glucose-targeting diet vs Mediterranean diet in pre-diabetics
“six-month dietary intervention in pre-diabetic individuals (NCT03222791)” — abstract:37666816 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
198 of 198 people sampled more than once (706 samples; median 4, up to 4 per person). Schedule stated by the source: “Stool and plaque samples taken before and after the six-month intervention period; followed by a six-month follow-up period (phase two).”; stated follow-up 12 mo.
Genera, mean relative abundance over 285 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 | 706 | 100% | ||||
| country | 706 | 100% | 706 | |||
| health_condition | 706 | 100% | 706 | |||
| subject_id | 706 | 100% | 706 | |||
| antibiotic_exposure | 706 | 100% | 706 | |||
| collection_date | 706 | 100% | 706 | |||
| detailed_location | 706 | 100% | ||||
| health_condition_detail | 706 | 100% | 706 | |||
| location_site | 706 | 100% | 706 | |||
| timepoint_label | 706 | 100% | 706 | |||
| intervention | 702 | 99% | 702 |
- An extracardiac unruptured right sinus of valsalva aneurysm complicated with atherothrombosis. 2016 PMID 27249813 PMC5323868 own_data
- Impact of dietary interventions on pre-diabetic oral and gut microbiome, metabolites and cytokines. 2023 PMID 37666816 PMC10477304 own_data
- Cross-body site microbial interactions influence the human plasma metabolome. 2026 PMID 41952172 PMC13181886 unsure
Archive description
Diabetes and associated comorbidities are a global health threat on the rise. We conducted a six-month dietary intervention in pre-diabetic individuals (NCT03222791), to mitigate the hyperglycemia and enhance metabolic health. The current work explores early diabetes markers in the 200 individuals who completed the trial. We find 166 of 2,803 measured features, including oral and gut microbial species and pathways, serum metabolites and cytokines, show significant change in response to a personalized postprandial glucose-targeting diet or the standard of care Mediterranean diet. These changes include established markers of hyperglycemia as well as novel features that can now be investigated as potential therapeutic targets. Our results indicate the microbiome mediates the effect of diet on glycemic, metabolic and immune measurements, with gut microbiome compositional change explaining 12.25% of serum metabolites variance. Although the gut microbiome displays greater compositional changes compared to the oral microbiome, the oral microbiome demonstrates more changes at the genetic level, with trends dependent on environmental richness and species prevalence in the population. In conclusion, our study shows dietary interventions can affect the microbiome, cardiometabolic profile and immune response of the host, and that these factors are well associated with each other, and can be harnessed for new therapeutic modalities. Nature communications https://doi.org/10.1038/s41467-023-41042-x
How this project entered the registry
Classified as human gut / stool / oral cavity shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.71. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.title · “oral and gut microbiome”
- life stage study.description · “pre-diabetic individuals”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA114241006 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | use of antibiotics three months before enrollment |
| SAMEA114241006 | collection_date | 2017-01-01 | R1 | 0.90 | biosample.attribute:collection_date | 2017-01-01 |
| SAMEA114241006 | country | IL | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Israel |
| SAMEA114241006 | health_condition | type2_diabetes | R4 | 0.45 | study.description | pre-diabetic individuals |
| SAMEA114241006 | health_condition_detail | Pre-diabetic; early diabetes markers explored | R4 | 0.45 | study.description | pre-diabetic individuals |
| SAMEA114241006 | intervention | diet_intervention | R2 | 0.75 | paper.supp.41467_2023_41042_MOESM9_ESM.xlsx[diet!Diet] | PPT diet |
| SAMEA114241006 | location_site | Weizmann Institute of Science | R3 | 0.70 | paper.fulltext.methods | invited for a visit at the trial's site |
| SAMEA114241006 | subject_id | 1 | R1 | 0.70 | sample.name_rule:alias | Gut_1_Post |
| SAMEA114241006 | timepoint_label | post | R1 | 0.70 | sample.name_rule:alias | Gut_1_Post |
Sequencing
706 runs over 706 samples · mean 0.92 Gbp per run (median 0.91 Gbp, total 650.40 Gbp; 706 runs with a base count) · layout SINGLE 706 · platform ILLUMINA 706 · models NextSeq 500 (454), Illumina NovaSeq 6000 (252) · 40% of runs with a Sandpiper profile · first public 2023-08-27
Authors (23)
Zhang J first · Liu Y · Liu L · Deng Y last · Shoer S first · Shilo S · Godneva A · Ben-Yacov O · Rein M · Wolf BC · Lotan-Pompan M · Bar N · Weiss EI · Houri-Haddad Y · Pilpel Y · Weinberger A · Segal E last · Jiang C · Zhou X · Gao P · Wong S · Snyder M · Shen X last
Downloads
PRJEB64861.csv.gz (17.1 KB) · parquet (94.1 KB) — all 706 samples, every field with route and confidence · PRJEB64861_determinations.csv.gz (39.7 KB) — 6,350 evidence rows