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PRJNA1156897 SRP530689

Gut microbiome in SLE patients, case-control, New York, USA

Metagenomic Profiling of Microbiomes from Patients with Autoimmune Diseases

129 stool metagenome samples from patients with systemic lupus erythematosus (SLE) collected in New York, USA, examining gut dysbiosis in a case-control study design. machine-written summary

129 samples · 129 runs · US · Age unknown · 2024 · 2.44 Gbp / sample

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Sources
✓Sequence archive 802○Abstract / description○Full text○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 archive802 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude, subject id)
○ Abstract / descriptionread; no usable statement
○ Full textread; no usable statement or table · PMC13247269
○ Supplementary tablesfiles read; no table could be matched to the samples
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet · share metadata
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
1 sampling locations · 1 country
Age
unknown129
Condition
autoimmune_inflammatory32
Country
US129
Body site
primary129
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 %)this project, 0.03–0.1 Gbp: 1 samplesall 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: 2 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 108 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 17 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 2.44 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinal — not resolved

21 of 36 people sampled more than once (58 samples; median 3, up to 4 per person).

How longitudinal and relatedness information is derived

Community composition
Bacteroides 10.7%Blautia_A 7.9%Bifidobacterium 6.4%Alistipes 5.5%Phocaeicola 4.8%Collinsella 4.0%Roseburia 3.0%Faecalibacterium 2.8%Anaerostipes 2.2%Ruminococcoides 2.2%Gemmiger 2.1%Parabacteroides 2.0%not assigned to a genus 6.0%other genera 40.4%

Genera, mean relative abundance over 115 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category0 0%
country129 100%129
health_condition32 25%32
subject_id73 57%73
collection_date129 100%129
detailed_location129 100%
latitude129 100%129
location_region129 100%129
longitude129 100%129
health_condition_detail32 25%32
timepoint_label20 16%20
Papers (1)
  • Multiomics-guided discovery of protective microbiome signatures in lupus-prone mice treated with Faecalibacterium prausnitzii. 2026 PMID 41974712 PMC13247269 unsure
Details
Archive description

Metagenomic sequencing of stool samples collected from patients with autoimmune diseases

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.

  • host run.host_tax_id · “9606”
  • body site study.description · “stool samples collected from patients”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN43502221collection_date2022-06R10.90biosample.attribute:collection_date2022-06
SAMN43502221countryUSR10.90sample.attr.geo_loc_nameUSA: NY
SAMN43502278health_conditionautoimmune_inflammatoryR10.70sample.name_rule:aliasSLE01v1_1_10_15_S33
SAMN43502278health_condition_detailSLE01v1_1_10_15_S33R10.70sample.name_rule:aliasSLE01v1_1_10_15_S33
SAMN43502221latitude42.4400R10.90biosample.attribute:lat_lon42.44 N 76.50 W
SAMN43502221location_regionNew YorkR10.75biosample.attribute:geo_loc_nameUSA: NY
SAMN43502221longitude-76.5000R10.90biosample.attribute:lat_lon42.44 N 76.50 W
SAMN43502272subject_idNOR09R10.70sample.name_rule:aliasNOR09v1_071316_78mg_S20
SAMN43502310timepoint_labelBR10.70sample.name_rule:alias131232_B_032514_0_337g_S76
Sequencing

129 runs over 129 samples · mean 2.39 Gbp per run (median 2.44 Gbp, total 308.29 Gbp; 129 runs with a base count) · layout SINGLE 78, PAIRED 51 · platform ILLUMINA 129 · models Illumina NovaSeq 6000 (129) · 89% of runs with a Sandpiper profile · first public 2024-09-10 – 2024-09-17

Authors (10)

Zhao N first · Geng P · Jimenez D · Garcia AC · Six N · LaPlante CI · Perez AG · Silverman GJ · Morel L · Ge Y last

Help complete this project

2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata

Downloads

PRJNA1156897.csv.gz (4.4 KB) · parquet (75.9 KB) — all 129 samples, every field with route and confidence · PRJNA1156897_determinations.csv.gz (7.1 KB) — 802 evidence rows

Samples (129 · every field this project has values for · hover a cell for its source)
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