Microbiome & osteoporosis in older US white women

Understanding Gut Microbiome's Impact on Osteoporosis

59 fecal samples from white women aged 60+ in the Louisiana Osteoporosis Study (New Orleans area, USA), a cross-sectional study examining the gut microbiome's relationship to bone mineral density/osteoporosis. machine-written summary

59 samples · 59 runs · US · Adult · 2023 · 4.97 Gbp / sample

ENA BioProject Sample sheet Registry Download Flag an issue

Sources

✓Sequence archive 531✓Abstract / description 118○Full text○Supplementary tables✓External resources 118–User contribution–Human verified

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

what each source gave

✓ Sequence archive	531 sample values (age, bmi, country, latitude, location locality, location region, longitude, sex)
✓ Abstract / description	118 sample values (location site, subject id)
○ Full text	read; no usable statement or table · PMC10611739
○ Supplementary tables	files read; no table could be matched to the samples
✓ External resources	118 sample values (health condition, health condition detail) · from GMrepo v3
– User contribution	nothing uploaded yet
– Human verified	not yet checked by a person · I checked this project — verify it

Samples at a glance

1 sampling locations · 1 country

Age

elderly33

adult26

Condition

other_disease59

Sex

female59

Country

US59

Body site

primary59

Sequencing depth per sample · this project all projects

Community composition

Bacteroides 22.5%Phocaeicola 14.1%Alistipes 8.1%Prevotella 4.7%Faecalibacterium 3.4%Parabacteroides 3.1%Roseburia 2.0%Oscillibacter 1.3%Vescimonas 1.2%Akkermansia 1.1%Escherichia 1.1%Acetatifactor 1.1%not assigned to a genus 5.1%other genera 31.0%

Genera, mean relative abundance over 55 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	R4
age_category	59	100%
country	59	100%	59
health_condition	59	100%		59
subject_id	59	100%			59
age_at_collection_days	59	100%	59
bmi	59	100%	59
detailed_location	59	100%
health_condition_detail	59	100%		59
latitude	59	100%	59
location_locality	59	100%	59
location_region	59	100%	59
location_site	59	100%			59
longitude	59	100%	59
sex	59	100%	59
smoking_status	59	100%	59

Papers (1)

Gut microbiota impacts bone via Bacteroides vulgatus-valeric acid-related pathways. 2023 PMID 37891329 PMC10611739 unsure

Details

Archive description

A total of 59 white females aged 60 years or older were recruited from the ongoing Louisiana Osteoporosis Study, which aims to establish a large sample pool in the greater New Orleans and surrounding areas of Southern Louisiana, USA, for investigating genetic and environmental factors related to musculoskeletal disorders. This study has been approved by the institutional review board of Tulane University (New Orleans, LA, USA), and each participant provided written consent before data and biosample collection. Individuals with pathological conditions that may affect bone mineral density (e.g., bilateral oophorectomy, chronic renal failure, liver failure, lung diseases, gastrointestinal diseases, and inherited bone diseases), or factors that may impact the gut microbiome (e.g., antibiotic use, gastroenteritis, major surgery requiring hospitalization, and intercontinental travel within the past three months), were excluded. The metagenomic shotgun sequencing of the collected fecal samples was performed by the Alkek Center for Metagenomics and Microbiome Research at Baylor College of Medicine.

How this project entered the registry

Classified as human gut / stool / lower respiratory / blood / tissue / internal fluids / 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.title · “Understanding Gut Microbiome's Impact on”
body site study.description · “failure, lung diseases, gastrointestinal diseases, and inherited”
body site study.description · “failure, liver failure, lung diseases, gastrointestinal diseases,”
body site study.description · “chronic renal failure, liver failure, lung diseases,”
body site study.description · “that may affect bone mineral density (e.g.,”
life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
life stage sample.attr.age · “60.54520548 (n=31/59)”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN35823316	age_at_collection_days	23330.0	R1	0.85	sample.attr.age	63.83013699
SAMN35823316	bmi	23.76	R1	0.90	sample.attr.bmi	23.75753341
SAMN35823316	country	US	R1	0.90	sample.attr.geo_loc_name	USA: New Orleans
SAMN35823316	health_condition	other_disease	R2	0.75	external.gmrepo source	phenotype: Osteoporosis
SAMN35823316	health_condition_detail	Osteoporosis	R2	0.75	external.gmrepo source	phenotype: Osteoporosis
SAMN35823316	latitude	29.9500	R1	0.90	biosample.attribute:lat_lon	29.95 N 90.07 W
SAMN35823316	location_locality	New Orleans	R1	0.85	biosample.attribute:geo_loc_name	USA: New Orleans
SAMN35823316	location_region	Louisiana	R1	0.60	biosample.attribute:lat_lon	29.95 N 90.07 W
SAMN35823316	location_site	Louisiana Osteoporosis Study	R4	0.45	ena.study_description	the ongoing Louisiana Osteoporosis Study
SAMN35823316	longitude	-90.0700	R1	0.90	biosample.attribute:lat_lon	29.95 N 90.07 W
SAMN35823316	sex	female	R1	0.70	sample.name_rule:title	Metagenome or environmental sample from human gut metagenome
SAMN35823316	smoking_status	never	R1	0.80	biosample.attribute:smoke	False
SAMN35823316	subject_id	SAMN35823316	R4	0.60	design.one_sample_per_subject:description	A total of 59 white females aged 60 years or older were recruited from the ongoing Louisiana Osteoporosis Study

Sequencing

59 runs over 59 samples · mean 4.88 Gbp per run (median 4.97 Gbp, total 288.03 Gbp; 59 runs with a base count) · layout PAIRED 59 · platform ILLUMINA 59 · models Illumina HiSeq X (59) · 93% of runs with a Sandpiper profile · first public 2023-08-30

Authors (32)

Lin X first · Xiao HM · Liu HM · Lv WQ · Greenbaum J · Gong R · Zhang Q · Chen YC · Peng C · Xu XJ · Pan DY · Chen Z · Li ZF · Zhou R · Wang XF · Lu JM · Ao ZX · Song YQ · Zhang YH · Su KJ · Meng XH · Ge CL · Lv FY · Luo Z · Shi XM · Zhao Q · Guo BY · Yi NJ · Shen H · Papasian CJ · Shen J · Deng HW last

Downloads

PRJNA986283.csv.gz (3.2 KB) · parquet (74.3 KB) — all 59 samples, every field with route and confidence · PRJNA986283_determinations.csv.gz (7.8 KB) — 767 evidence rows

Samples (59 · every field this project has values for · hover a cell for its source)

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