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PRJNA672125 SRP289701

Gut microbiome in postmenopausal osteoporosis, New Zealand

Bugs and Bones

86 fecal metagenome samples from postmenopausal women in Palmerston North, New Zealand, classified as healthy, osteopenic, or osteoporotic; case-control study comparing gut microbiome composition and function across groups. machine-written summary

86 samples · 344 runs · NZ · Adult · 2021 · 2.77 Gbp / sample

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Sources
✓Sequence archive 430○Abstract / description✓Full text 344○Supplementary tables✓External resources 172–User contribution–Human verified

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

what each source gave
✓ Sequence archive430 sample values (age, bmi, collection date, country, location locality)
○ Abstract / descriptionread; no usable statement
✓ Full text344 sample values (antibiotic exposure, location site, sex, subject id) · PMC7990138
○ Supplementary tablesfiles read; no table could be matched to the samples
✓ External resources172 sample values (health condition, health condition detail) · from GMrepo v3
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
1 country
Age
adult58
elderly28
Condition
other_disease86
Sex
female86
Country
NZ86
Body site
primary86
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: 55 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 31 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 2.77 Gbp per sample0130Gbp
Community composition
Blautia_A 7.9%Roseburia 7.4%Bacteroides 5.5%Faecalibacterium 3.4%Phocaeicola 2.8%Coprococcus 2.7%Ruminococcoides 2.2%Alistipes 1.9%Fusicatenibacter 1.9%Gemmiger 1.6%Anaerobutyricum 1.5%Streptococcus 1.4%not assigned to a genus 16.9%other genera 43.1%

Genera, mean relative abundance over 86 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category86 100%
country86 100%86
health_condition86 100%86
subject_id86 100%86
age_at_collection_days86 100%86
antibiotic_exposure86 100%86
bmi86 100%86
collection_date86 100%86
detailed_location86 100%
health_condition_detail86 100%86
location_locality86 100%86
location_site86 100%86
sex86 100%86
Papers (1)
  • The Gut Microbiome Is Altered in Postmenopausal Women With Osteoporosis and Osteopenia. 2021 PMID 33778322 PMC7990138 own_data
Details
Archive description

Study to look at the gut microbiomes of post-menopausal women with osteoporosis/osteopenia.

How this project entered the registry

Classified as human gut / stool / other human site 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.description · “look at the gut microbiomes of post-menopausal”
  • body site external_curation.infant_catalog · “body_site_call gut/stool”
  • body site study.title · “Bugs and Bones”
  • life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
  • life stage study.description · “microbiomes of post-menopausal women with osteoporosis/osteopenia.”
  • life stage sample.attr.age · “62 (n=42/86)”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN16557025age_at_collection_days23010.8R10.70sample.attr.age63
SAMN16557025antibiotic_exposurenoR30.70paper.fulltext.methodsuse of antibiotics within 3 months of the study
SAMN16557025bmi24.11R10.90sample.attr.bmi24.1147252
SAMN16557025collection_date2017-10-17/2018-03-06R10.90biosample.attribute:collection_date2017-10-17/2018-03-06
SAMN16557025countryNZR10.90sample.attr.geo_loc_nameNew Zealand: Palmerston North
SAMN16557025health_conditionother_diseaseR20.75external.gmrepo sourcephenotype: Osteoporosis, Postmenopausal
SAMN16557025health_condition_detailOsteoporosis, PostmenopausalR20.75external.gmrepo sourcephenotype: Osteoporosis, Postmenopausal
SAMN16557025location_localityPalmerston NorthR10.85biosample.attribute:geo_loc_nameNew Zealand: Palmerston North
SAMN16557025location_siteHuman Nutrition Unit, Massey UniversityR30.70paper.fulltext.methodsHuman Nutrition Unit of Massey University, Palmerston North
SAMN16557025sexfemaleR30.60paper.fulltext.results86 postmenopausal women were analyzed
SAMN16557025subject_idSAMN16557025R30.70design.one_sample_per_subject:fulltextEighty‐six postmenopausal women aged 54 to 81 years participated in phase II of the "Bugs'n'Bones" study
Sequencing

344 runs over 86 samples · mean 0.70 Gbp per run (median 0.69 Gbp, total 242.39 Gbp; 344 runs with a base count) · layout PAIRED 344 · platform ILLUMINA 344 · models Illumina HiSeq 2500 (344) · 92% of runs with a Sandpiper profile · first public 2021-01-23

Authors (5)

Rettedal EA first · Ilesanmi-Oyelere BL · Roy NC · Coad J · Kruger MC last

Downloads

PRJNA672125.csv.gz (3.8 KB) · parquet (76.0 KB) — all 86 samples, every field with route and confidence · PRJNA672125_determinations.csv.gz (8.5 KB) — 946 evidence rows

Samples (86 · every field this project has values for · hover a cell for its source)
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