Home › Studies › PRJNA962059
PRJNA962059 SRP434593

Gut microbiome in Lewy body dementia, Minnesota case-control

Lewy Body Dementia Microbiome

77 samples from Rochester, Minnesota, comparing gut microbiota of Lewy body dementia and REM sleep behavior disorder cases with cohabitant and non-cohabitant healthy controls, using 16S rRNA sequencing in a case-control design. machine-written summary

77 samples · 77 runs · US · Age unknown · 2024 · 3.36 Gbp / sample

ENABioProjectSample sheetRegistryDownloadFlag an issue

Sources
✓Sequence archive 755✓Abstract / description 3✓Full text 77○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 archive755 sample values (age, collection date, country, health condition, health condition detail, latitude, location locality, location region)
✓ Abstract / description3 sample values (health condition detail)
✓ Full text77 sample values (subject id) · PMC11614677
○ 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
Samples at a glance
1 sampling locations · 1 country
Age
elderly38
adult36
unknown3
Condition
healthy_control39
neurological_psychiatric35
Sex
female40
male34
Country
US77
Body site
primary77
Collected 2019–2021
2019: 37 samples2020: 25 samples2021: 12 samples20192021
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)this project, 0–0.03 Gbp: 1 samplesall 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 %)this project, 0.3–1 Gbp: 1 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: 56 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)all 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 3.36 Gbp per sample0130Gbp
Sampling design and relatedness

households — not resolved

Lewy body disease cases and cohabitant controls (cohabiting pairs); pairing not deposited.

How longitudinal and relatedness information is derived

Community composition
Blautia_A 11.2%Bacteroides 5.7%Bifidobacterium 3.9%Alistipes 3.8%Collinsella 3.6%Faecalibacterium 3.5%Ruminococcoides 3.4%Streptococcus 2.6%Phocaeicola 2.6%Roseburia 2.6%Gemmiger 2.3%Akkermansia 2.2%not assigned to a genus 7.0%other genera 45.6%

Genera, mean relative abundance over 70 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category74 96%
country77 100%77
health_condition74 96%74
subject_id77 100%77
detailed_location77 100%
health_condition_detail77 100%743
latitude77 100%77
location_locality77 100%77
location_region77 100%77
longitude77 100%77
age_at_collection_days74 96%74
collection_date74 96%74
sex74 96%74
Papers (1)
  • Taxonomic intestinal microbiota differences in Lewy body spectrum disease and cohabitant controls. 2024 PMID 39426329 PMC11614677 own_data
Details
Archive description

Characterization of the intestinal microbiota of patients with Lewy Body Dementia.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of elderly and adult by opus_adjudicated with confidence 0.80. Assay shotgun_dna.

  • host run.host_tax_id · “9606”
  • host study.description · “patients with Lewy Body Dementia”
  • body site study.description · “intestinal microbiota”
  • life stage sample.attr.age_at_visit · “68 (n=44/77)”
  • life stage sample.attr.age_at_visit · “63 (n=30/77)”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN34377922age_at_collection_days24471.8R10.70sample.attr.age_at_visit67
SAMN34377922collection_date2019-05-14R10.90biosample.attribute:collection_date2019-05-14
SAMN34377922countryUSR10.90sample.attr.geo_loc_nameUSA: Rochester, Minnesota
SAMN34377922health_conditionneurological_psychiatricR10.90biosample_attrLBD
SAMN34377922health_condition_detailCaseR10.90sample.attr.overallgroupCase
SAMN40203027health_condition_detailmixed_case_control: Lewy Body Dementia and iRBD cases vs cohabitant and non-cohabitant controlsR40.50study.descriptionLewy Body Dementia
SAMN34377922latitude44.0222R10.90biosample.attribute:lat_lon44.0222 N 92.0333 W
SAMN34377922location_localityRochesterR10.85biosample.attribute:geo_loc_nameUSA: Rochester, Minnesota
SAMN34377922location_regionMinnesotaR10.85biosample.attribute:geo_loc_nameUSA: Rochester, Minnesota
SAMN34377922longitude-92.0333R10.90biosample.attribute:lat_lon44.0222 N 92.0333 W
SAMN34377922sexmaleR10.90sample.attr.sexmale
SAMN34377922subject_idSAMN34377922R30.70design.one_sample_per_subject:fulltext16S rRNA amplicon sequencing was performed in 38 cases (27 LBD, 11 iRBD) and 39 cohabitant controls
Sequencing

77 runs over 77 samples · mean 3.44 Gbp per run (median 3.36 Gbp, total 264.81 Gbp; 77 runs with a base count) · layout PAIRED 77 · platform ILLUMINA 77 · models Illumina NovaSeq 6000 (77) · 91% of runs with a Sandpiper profile · first public 2024-03-13

Authors (19)

Teigen LM first · McCarter SJ · Ziegert Z · Staley C · Grant KM · Gupta VK · Zhao X · St Louis EK · Kantarci K · Lowe VJ · Forsberg LK · Savica R · Ramanan VK · Jones DT · Petersen RC · Sung J · Khoruts A · Boeve BF · Ross OA last

Downloads

PRJNA962059.csv.gz (3.7 KB) · parquet (75.6 KB) — all 77 samples, every field with route and confidence · PRJNA962059_determinations.csv.gz (6.8 KB) — 835 evidence rows

Samples (77 · every field this project has values for · hover a cell for its source)
Loading the sample table…