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PRJEB76849 ERP161337

Gut microbiome diet intervention in cognitive impairment/AD, USA

Gut microbiome alterations in Alzheimers disease _WF-BEAM

101 fecal and blood samples from a diet intervention study in people with cognitive impairment and Alzheimer's disease, collected mainly in North Carolina with some from San Diego, CA, USA; intervention design. machine-written summary

101 samples · 107 runs · US · Adult · 2024 · 7.19 Gbp / sample

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Sources
✓Sequence archive 1,358○Abstract / description✓Full text 218○Supplementary tables–External resources–User contribution–Human verified

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

what each source gave
✓ Sequence archive1,358 sample values (age, bmi, collection date, country, health condition, health condition detail, intervention, intervention detail)
○ Abstract / descriptionread; no usable statement
✓ Full text218 sample values (antibiotic exposure, health condition, health condition detail, location site) · PMC11216994
○ Supplementary tablesfiles read; no table could be matched to the samples
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Interventions

intervention · arms resolved

before · no interventionbefore · no interventi39 samplesdietdiet54 samples
single arm: samples before and on the intervention

19 people have samples in more than one arm.

Controlled / prescribed diet or feeding regimen design single_arm_before_after · population neurological_psychiatric · Diet intervention in cognitive impairment/AD patients

“fecal and blood samples from a diet intervention” — bioproject.description (study level; per-sample arms are in the intervention column below)

Samples at a glance
2 sampling locations · 1 country
Age
adult73
elderly28
Condition
healthy_control55
neurological_psychiatric38
cardiometabolic_other8
Sex
female69
male24
Country
US101
Body site
primary93
unknown8
Collected 2015–2021
2015: 50 samples2016: 39 samples2017: 4 samples2021: 8 samples20152021
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)this project, 0–0.03 Gbp: 4 samplesall projects, 0.03–0.1 Gbp: 17,066 samples (3 %)this project, 0.03–0.1 Gbp: 3 samplesall projects, 0.1–0.3 Gbp: 29,179 samples (5 %)this project, 0.1–0.3 Gbp: 3 samplesall projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 18 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 19 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 13 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 41 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 7.19 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinal

20 of 30 people sampled more than once (91 samples; median 5, up to 5 per person) · follow-up median 6 mo (max 7 mo) · median interval between samples 46 d (time from collection dates).

3AWFR0000813AWFR000081: day 03AWFR000081: day 423AWFR000081: day 853AWFR000081: day 1313AWFR000081: day 1743BCCR0010243BCCR001024: day 03BCCR001024: day 403BCCR001024: day 953BCCR001024: day 1333BCCR001024: day 1803BLFO0000403BLFO000040: day 03BLFO000040: day 493BLFO000040: day 913BLFO000040: day 1333BLFO000040: day 1753BSLA0007463BSLA000746: day 03BSLA000746: day 503BSLA000746: day 983BSLA000746: day 1493BSLA000746: day 1913CBSH0008273CBSH000827: day 03CBSH000827: day 763CBSH000827: day 1243CBSH000827: day 1743CBSH000827: day 2193CDMA0009513CDMA000951: day 03CDMA000951: day 623CDMA000951: day 1113CDMA000951: day 1533EHRI0007733EHRI000773: day 03EHRI000773: day 493EHRI000773: day 1073EHRI000773: day 1553EHRI000773: day 2193FHGO0003923FHGO000392: day 03FHGO000392: day 643FHGO000392: day 1113FHGO000392: day 1553FHGO000392: day 2053JACA0011523JACA001152: day 03JACA001152: day 523JACA001152: day 863JACA001152: day 1293JACA001152: day 1853JMCO0007223JMCO000722: day 03JMCO000722: day 603JMCO000722: day 1183JMCO000722: day 1403JMCO000722: day 2223JRWE0008813JRWE000881: day 03JRWE000881: day 573JRWE000881: day 1013JRWE000881: day 1483JXAL0003043JXAL000304: day 03JXAL000304: day 443JXAL000304: day 843JXAL000304: day 1263JXAL000304: day 1683KXCH0001693KXCH000169: day 03KXCH000169: day 573KXCH000169: day 1023KXCH000169: day 1513KXCH000169: day 1973LDMO0001253LDMO000125: day 03LDMO000125: day 423LDMO000125: day 843LDMO000125: day 1273LDMO000125: day 1923LDST0007723LDST000772: day 03LDST000772: day 423LDST000772: day 983LDST000772: day 1343LDST000772: day 1873MRHA0011533MRHA001153: day 03MRHA001153: day 473PXMC0011573PXMC001157: day 03PXMC001157: day 703PXMC001157: day 1113PXMC001157: day 1553RHHO0014723RHHO001472: day 03RHHO001472: day 553RHHO001472: day 963RHHO001472: day 1383RHHO001472: day 1813RLSI0011643RLSI001164: day 03RLSI001164: day 1593TFBO0008183TFBO000818: day 03TFBO000818: day 593TFBO000818: day 1053TFBO000818: day 1443TFBO000818: day 1860 d56 d4 mo5 mo7 mo

Each row is one person (20 shown); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition
Bacteroides 15.7%Phocaeicola 8.7%Alistipes 7.1%Akkermansia 3.4%Prevotella 3.3%Vescimonas 3.3%Parabacteroides 2.5%Faecalibacterium 2.4%Roseburia 1.7%Lachnospira 1.4%Oscillibacter 1.4%CAG-170 1.2%not assigned to a genus 7.8%other genera 40.0%

Genera, mean relative abundance over 68 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category101 100%
country101 100%101
health_condition101 100%938
subject_id101 100%101
antibiotic_exposure101 100%101
collection_date101 100%101
detailed_location101 100%
health_condition_detail101 100%938
latitude101 100%101
location_region101 100%101
location_site101 100%101
longitude101 100%101
age_at_collection_days93 92%93
bmi93 92%93
intervention93 92%93
intervention_detail93 92%93
sex93 92%93
timepoint_label93 92%93
location_locality8 8%8
Papers (1)
  • Serum and CSF metabolomics analysis shows Mediterranean Ketogenic Diet mitigates risk factors of Alzheimer's disease. 2024 PMID 38962750 PMC11216994 own_data
Details
Archive description

fecal and blood samples from a diet intervention in people with cognitive impairment and AD

How this project entered the registry

Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of adult 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 · “Gut microbiome alterations in”
  • body site study.description · “fecal and blood samples”
  • body site study.description · “fecal and blood samples from a”
  • life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMEA115767066age_at_collection_days22645.5R10.90sample.attr.age62
SAMEA115767066antibiotic_exposurenoR30.70paper.fulltext.methodsWritten informed consent was obtained from all participants
SAMEA115767066bmi27.92R10.90sample.attr.bmi_pbl27.92
SAMEA115767066collection_date2015-02-11R10.90biosample.attribute:collection_date2015-02-11
SAMEA115767066countryUSR10.90sample.attr.geographic_location_country_and_or_seaUSA
SAMEA115767066health_conditionneurological_psychiatricR10.85biosample.attribute:memdxmemdx: mci-a
SAMEA115767168health_conditioncardiometabolic_otherR30.70paper.body.methods_resultsAll participants had prediabetes according to the American Diabetes Association guidelines, with a screening hemoglobin A1c level of 5.7–6.4%
SAMEA115767066health_condition_detailmci-aR10.85biosample.attribute:memdxmemdx: mci-a
SAMEA115767168health_condition_detailprediabetesR30.70paper.body.methods_resultsAll participants had prediabetes according to the American Diabetes Association guidelines, with a screening hemoglobin A1c level of 5.7–6.4%
SAMEA115767066interventionno_interventionR10.80biosample.attribute:timepointtimepoint: pre 1
SAMEA115767067interventiondiet_interventionR10.90biosample.attribute:first_dietfirst_diet: 1
SAMEA115767068interventionno_interventionR10.80biosample.attribute:visit_typevisit_type: preb-cog
SAMEA115767066intervention_detailBaseline before first intervention; assigned arm: First diet intervention armR10.80biosample.attribute:timepointtimepoint: pre 1
SAMEA115767067intervention_detailFirst diet intervention armR10.90biosample.attribute:first_dietfirst_diet: 1
SAMEA115767068intervention_detailPre-intervention arm B cognitive visit; assigned arm: First diet intervention armR10.80biosample.attribute:visit_typevisit_type: preb-cog
SAMEA115767066latitude36.1000R10.90biosample.attribute:latitude+longitude36.1 -80.26
SAMEA115767168location_localitySan DiegoR10.85biosample.attribute:geo_loc_nameUSA:CA:San Diego
SAMEA115767066location_regionNorth CarolinaR10.85biosample.attribute:geo_loc_nameUSA:North Carolina
SAMEA115767066location_siteWake ForestR30.70paper.fulltext.methodsapproved by the Wake Forest Institutional Review Board
SAMEA115767066longitude-80.2600R10.90biosample.attribute:latitude+longitude36.1 -80.26
SAMEA115767066sexmaleR10.90sample.attr.sexmale
SAMEA115767066subject_id3AWFR000081R10.85sample.attr.host_subject_id3AWFR000081
SAMEA115767066timepoint_labelprea-cogR10.85sample.attr.visit_typeprea-cog
Sequencing

107 runs over 101 samples · mean 6.53 Gbp per run (median 6.24 Gbp, total 698.21 Gbp; 107 runs with a base count) · layout PAIRED 107 · platform ILLUMINA 107 · models Illumina NovaSeq 6000 (107) · 64% of runs with a Sandpiper profile · first public 2024-06-21 – 2024-06-25

Authors (0)

No author record.

Downloads

PRJEB76849.csv.gz (5.1 KB) · parquet (78.4 KB) — all 101 samples, every field with route and confidence · PRJEB76849_determinations.csv.gz (12.2 KB) — 1,576 evidence rows

Samples (101 · every field this project has values for · hover a cell for its source)
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