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PRJNA798058 SRP355475

Microbiome in preclinical Alzheimer's

The gut microbiome in preclinical Alzheimer Disease

164 gut metagenome samples from cognitively normal adults in St. Louis, USA, comparing 49 with biomarker evidence of preclinical Alzheimer's disease to 114 healthy controls, in a cross-sectional case-control design. machine-written summary

164 samples · 164 runs · US · Adult · 2022 · 4.97 Gbp / sample

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Sources
✓Sequence archive 984✓Abstract / description 279○Full text○Supplementary tables✓External resources 701–User contribution–Human verified

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

what each source gave
✓ Sequence archive984 sample values (collection date, country, latitude, location locality, location region, longitude)
✓ Abstract / description279 sample values (health condition detail, subject id)
○ Full textread; no usable statement or table · PMC10680783, PMC13035836
○ Supplementary tablesfiles read; no table could be matched to the samples
✓ External resources701 sample values (age, bmi, health condition, health condition detail, sex) · from Meta2DB (LLNL)
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
1 sampling locations · 1 country
Age
elderly164
Condition
healthy_control114
neurological_psychiatric49
Sex
female90
male73
Country
US164
Body site
primary164
Collected 2019–2021
2019: 9 samples2020: 123 samples2021: 32 samples20192021
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)all projects, 0.03–0.1 Gbp: 17,066 samples (3 %)all projects, 0.1–0.3 Gbp: 29,179 samples (5 %)all projects, 0.3–1 Gbp: 47,044 samples (8 %)all projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 24 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 134 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 6 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 4.97 Gbp per sample0130Gbp
Community composition
Blautia_A 10.7%Bacteroides 7.9%Roseburia 5.2%Ruminococcoides 3.7%Faecalibacterium 3.5%Phocaeicola 3.4%Mediterraneibacter 3.3%Alistipes 2.5%Anaerostipes 2.5%Collinsella 2.0%Streptococcus 1.8%Fusicatenibacter 1.7%not assigned to a genus 7.5%other genera 44.4%

Genera, mean relative abundance over 148 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category164 100%
country164 100%164
health_condition163 99%163
subject_id164 100%164
collection_date164 100%164
detailed_location164 100%
health_condition_detail164 100%49115
latitude164 100%164
location_locality164 100%164
location_region164 100%164
longitude164 100%164
age_at_collection_days163 99%163
bmi163 99%163
sex163 99%163
Papers (2)
  • Gut microbiome composition may be an indicator of preclinical Alzheimer's disease. 2023 PMID 37315112 PMC10680783 own_data
  • Cross-domain metabolic interactions link Methanobrevibacter smithii to colorectal cancer microbial ecosystems. 2026 PMID 41720792 PMC13035836 unsure
Details
Archive description

The current paradigm of Alzheimer Disease (AD) pathology builds on a progression from cognitively normal status, to cognitively normal with biomarker evidence of disease (preclinical AD), to symptomatic AD characterized by both abnormal biomarker levels and cognitive impairment. Recent work has demonstrated that the gut microbiomes of symptomatic AD patients have distinct taxonomic compositions compared to healthy cognitively normal controls. However, knowledge about changes in the gut microbiome prior to the onset of symptomatic AD is limited. In this cross-sectional study we compared the taxonomic composition, microbial functional potential, and abundances of metagenome-assembled genomes (MAGs) in a cohort of 43 cognitively normal individuals with preclinical AD and 50 cognitively normal individuals without evidence of AD. An observation of gut microbiome correlates of preclinical AD neuropathology has the potential to improve our understanding of AD etiology, enable the identification of gut-derived biomarkers of AD or AD risk, and inform the development of therapeutic interventions.

How this project entered the registry

Classified as human gut / stool 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 · “The gut microbiome in preclinical”
  • body site study.description · “demonstrated that the gut microbiomes of symptomatic”
  • life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN25046593age_at_collection_days31174.1R20.70external.meta2db sourcehost_age: 85.35
SAMN25046593bmi26.1689R20.70external.meta2db sourcehost_body_mass_index: 26.1688587582839 kilogram per meter squared
SAMN25046593collection_date2020R10.90biosample.attribute:collection_date2020
SAMN25046593countryUSR10.90sample.attr.geo_loc_nameUSA: St. Louis
SAMN25046593health_conditionneurological_psychiatricR20.70external.meta2db sourcealzheimers
SAMN25046593health_condition_detailalzheimersR20.70external.meta2db sourcealzheimers
SAMN25046594health_condition_detailmixed_case_control: preclinical Alzheimer Disease vs cognitively normal controlsR40.40study.description43 cognitively normal individuals with preclinical AD and 50 cognitively normal individuals
SAMN25046593latitude38.6270R10.90biosample.attribute:lat_lon38.6270 N 90.1994 W
SAMN25046593location_localitySt. LouisR10.85biosample.attribute:geo_loc_nameUSA: St. Louis
SAMN25046593location_regionMissouriR10.60biosample.attribute:lat_lon38.6270 N 90.1994 W
SAMN25046593longitude-90.1994R10.90biosample.attribute:lat_lon38.6270 N 90.1994 W
SAMN25046593sexmaleR20.70external.meta2db sourcehost_sex: male
SAMN25046593subject_idSAMN25046593R40.60design.one_sample_per_subject:abstractwe compared the taxonomic composition and gut microbial function in a cohort of 164 cognitively normal individuals
Sequencing

164 runs over 164 samples · mean 5.19 Gbp per run (median 4.97 Gbp, total 851.41 Gbp; 164 runs with a base count) · layout PAIRED 164 · platform ILLUMINA 164 · models Illumina NovaSeq 6000 (164) · 90% of runs with a Sandpiper profile · first public 2022-05-02 – 2023-01-01

Authors (39)

Ferreiro AL first · Choi J · Ryou J · Newcomer EP · Thompson R · Bollinger RM · Hall-Moore C · Ndao IM · Sax L · Benzinger TLS · Stark SL · Holtzman DM · Fagan AM · Schindler SE · Cruchaga C · Butt OH · Morris JC · Tarr PI · Ances BM · Dantas G last · Mohammadzadeh R first · Mahnert A · Zurabishvili T · Wink L · Kumpitsch C · Habisch H · Sprengel J · Filek K · Mertelj P · Pernitsch D · Hingerl K · Durdevic M · Gorkiewicz G · Diener C · Loy A · Kolb D · Trautwein C · Madl T · Moissl-Eichinger C last

Downloads

PRJNA798058.csv.gz (7.3 KB) · parquet (80.8 KB) — all 164 samples, every field with route and confidence · PRJNA798058_determinations.csv.gz (22.4 KB) — 1,964 evidence rows

Samples (164 · every field this project has values for · hover a cell for its source)
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