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PRJNA1086951 SRP630268

MIND Diet vs Control Trial, Fecal Metagenomics, Chicago

MIND Study - Fecal Metagenomics

638 fecal metagenome samples from elderly participants in Chicago, IL, comparing a MIND diet intervention cohort to a healthy control group over a four-year longitudinal dietary intervention study. machine-written summary

638 samples · 638 runs · US · Adult · 2025 · 2.45 Gbp / sample

ENA BioProject Sample sheet Registry Download Flag an issue

Sources

✓Sequence archive 7,779○Abstract / description✓Full text 313✓Supplementary tables 2,100–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave

✓ Sequence archive	7,779 sample values (age, bmi, collection date, country, diet, diet detail, intervention, intervention detail)
○ Abstract / description	read; no usable statement
✓ Full text	313 sample values (health condition) · PMC13060763
✓ Supplementary tables	2,100 sample values (health condition, health condition detail, subject id, timepoint)
– 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

Interventions

intervention · arms resolved

randomised to parallel arms

Controlled / prescribed diet or feeding regimen design randomized_controlled_trial · MIND diet vs control diet with caloric restriction, up to 3 years

“control and mind-diet research participants” — bioproject.description (study level; per-sample arms are in the intervention column below)

Samples at a glance

1 sampling locations · 1 country

Age

elderly638

Condition

healthy_control325

intervention_cohort313

Sex

female444

male194

Country

US638

Body site

primary638

Collected 2017–2020

Sequencing depth per sample · this project all projects

! Self-contradictory metadata

age: two sequence archives disagree for 2 samples (e.g. 79.0 vs 28779.3) — withheld.

The sources disagree on 2 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).

Contradicted values (2)

sample	field	value	other value	handling
SAMN51823646	age	79.0 (sequence archive)	28779.3 (sequence archive)	withheld: neither value published
SAMN51823809	age	71.5 (sequence archive)	26129.8 (sequence archive)	withheld: neither value published

Sampling design and relatedness

longitudinal

187 of 214 people sampled more than once (611 samples; median 3, up to 4 per person) · follow-up median 2.9 y (max 3.2 y) · median interval between samples 12 mo (time from age at collection).

Each row is one person (36 shown of 187); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition

Bacteroides 10.9%Phocaeicola 6.1%Akkermansia 6.0%Alistipes 5.5%Roseburia 3.2%Vescimonas 2.5%Dialister 2.5%Gemmiger 2.5%Imtechella 2.0%Ruminococcoides 1.9%Faecalibacterium 1.7%Prevotella 1.5%not assigned to a genus 8.8%other genera 44.9%

Genera, mean relative abundance over 634 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage

field	samples	coverage	R1	R2	R3
age_category	638	100%
country	638	100%	638
health_condition	638	100%		325	313
subject_id	638	100%	1	637
bmi	638	100%	638
collection_date	638	100%	638
detailed_location	638	100%
health_condition_detail	638	100%		638
intervention	638	100%	638
intervention_detail	638	100%	638
latitude	638	100%	638
location_locality	638	100%	638
location_region	638	100%	638
longitude	638	100%	638
sex	638	100%	638
timepoint_label	638	100%	138	500
age_at_collection_days	636	100%	636
diet	312	49%	312
diet_detail	312	49%	312

Papers (1)

Weight loss and metabolic improvements dominate the microbiome response in the MIND diet intervention: a randomized controlled trial. 2026 PMID 41958469 PMC13060763 own_data

Details

Archive description

Four-year study examining both control and mind-diet research participants. Fecal shotgun metagenomics. Removal of human data.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of adult and elderly by deterministic_prior with confidence 0.90. Assay shotgun_dna.

host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
body site study.title · “MIND Study - Fecal Metagenomics”
body site study.description · “mind-diet research participants. Fecal shotgun metagenomics. Removal”
life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
life stage sample.attr.host_age · “66.48049281 (n=593/638)”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN51823393	age_at_collection_days	26869.4	R1	0.85	sample.attr.host_age	73.62080767
SAMN51823393	bmi	29.62	R1	0.90	sample.attr.host_body_mass_index	29.61659449
SAMN51823393	collection_date	2017	R1	0.90	biosample.attribute:collection_date	2017
SAMN51823393	country	US	R1	0.90	sample.attr.geo_loc_name	USA: Chicago, IL
SAMN51823411	diet	therapeutic_or_study_diet	R1	0.70	biosample.attribute:host_diet	MIND
SAMN51823411	diet_detail	MIND	R1	0.70	biosample.attribute:host_diet	MIND
SAMN51823393	health_condition	healthy_control	R2	0.80	paper.supp.TRC2-12-e70239-s006.xlsx[Metadata!Group]	Control
SAMN51823411	health_condition	intervention_cohort	R3	0.70	paper.fulltext.methods	3‐year, randomized controlled trial comparing the MIND diet
SAMN51823393	health_condition_detail	Control	R2	0.85	paper.supp.TRC2-12-e70239-s006.xlsx[Metadata!Group]	Control
SAMN51823393	intervention	no_intervention	R1	0.90	biosample.attribute:host_diet	host_diet: Control
SAMN51823393	intervention_detail	control diet group	R1	0.90	biosample.attribute:host_diet	host_diet: Control
SAMN51823393	latitude	41.8781	R1	0.90	biosample.attribute:lat_lon	41.8781 N 87.6298 W
SAMN51823393	location_locality	Chicago	R1	0.85	biosample.attribute:geo_loc_name	USA: Chicago, IL
SAMN51823393	location_region	Illinois	R1	0.75	biosample.attribute:geo_loc_name	USA: Chicago, IL
SAMN51823393	longitude	-87.6298	R1	0.90	biosample.attribute:lat_lon	41.8781 N 87.6298 W
SAMN51823393	sex	female	R1	0.90	sample.attr.host_sex	female
SAMN51823869	subject_id	MIND_BL	R1	0.85	sample.attr.host_subject_id	MIND_BL
SAMN51823393	subject_id	211021	R2	0.70	sample.name_rule:library_name	library_name 211021-BL_S41
SAMN51823393	timepoint_label	baseline	R1	0.85	biosample.attribute:description	description: BL
SAMN51823869	timepoint_label	baseline	R1	0.70	sample.name_rule:library_name	278013-BL_S49
SAMN51823394	timepoint_label	Y1	R2	0.85	paper.supp.TRC2-12-e70239-s006.xlsx[Metadata!Visit]	Y1

Sequencing

638 runs over 638 samples · mean 2.49 Gbp per run (median 2.45 Gbp, total 1,586.09 Gbp; 638 runs with a base count) · layout PAIRED 638 · platform ILLUMINA 638 · models Illumina NovaSeq 6000 (638) · 99% of runs with a Sandpiper profile · first public 2025-10-02 – 2025-10-05

Authors (12)

Voigt RM first · Chaudhary A · Naqib A · Engen PA · Adnan D · Dhana K · Green SJ · Villanueva M · Agarwal P · Barnes LL · Sacks F · Keshavarzian A last

Downloads

PRJNA1086951.csv.gz (26.1 KB) · parquet (106.5 KB) — all 638 samples, every field with route and confidence · PRJNA1086951_determinations.csv.gz (85.8 KB) — 10,192 evidence rows

Samples (638 · every field this project has values for · hover a cell for its source)

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