Gut bacterial & fungal microbiome in SLE, China
284 fecal metagenome samples from treatment-naïve SLE patients and matched healthy controls in China, with some post-treatment samples, examining gut bacterial dysbiosis and mycobiome alterations in systemic lupus erythematosus; case-control design. machine-written summary
284 samples · 284 runs · CN · Age unknown · 2020 · 11.53 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,988 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 284 sample values (antibiotic exposure) · PMC12771783, PMC13247269 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
Schedule stated by the source: “117 untreated SLE patients sampled; 52 of these had a post-treatment follow-up fecal sample” (time origin: intervention_start).
Genera, mean relative abundance over 262 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 284 | 100% | 284 | |||
| health_condition | 284 | 100% | 284 | |||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 284 | 100% | 284 | |||
| collection_date | 284 | 100% | 284 | |||
| detailed_location | 284 | 100% | ||||
| health_condition_detail | 284 | 100% | 284 | |||
| latitude | 284 | 100% | 284 | |||
| location_region | 284 | 100% | 284 | |||
| longitude | 284 | 100% | 284 |
- Altered gut mycobiome and cross-kingdom microbial interactions in systemic lupus erythematosus. 2025 PMID 41318497 PMC12771783 own_data
- Multiomics-guided discovery of protective microbiome signatures in lupus-prone mice treated with Faecalibacterium prausnitzii. 2026 PMID 41974712 PMC13247269 unsure
Archive description
Gut microbiota is closely implicated with the development and function of host immune system1. Systemic lupus erythematosus (SLE), characterized by chronic inflammation and multi-organ damage, has been suggested to associate with gut dysbiosis, but knowledge is limited from small sample size and 16s rRNA-based studies. To shed new light on the role of microbiota in SLE development, we analyzed the fecal metagenome of 117 treatment-naïve SLE patients and 115 sex- and age-matched healthy controls (HC) by deep-sequencing in addition, 52 of the aforementioned patients have post-treatment fecal metagenome for comparison. We found significant difference in microbial composition and function between SLE and HC, revealing multiple plausible contributing bacterial species and metabolic pathways in SLE. In-depth SNP-based analysis revealed an oral-microbiome origin for two marker species, strengthening the importance of bacterial translocation in disease development. Lastly, we confirmed experimentally that peptides of SLE-enriched species mimicking autoantigens such as Sm can trigger autoimmune T-cell responses, suggesting a potentially causal role of gut microbiota in SLE.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.85. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “analyzed the fecal metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11273759 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | abstained from antibiotics or probiotics for at least three months |
| SAMN11273759 | collection_date | 2018-04-01 | R1 | 0.90 | biosample.attribute:collection_date | 2018-04-01 |
| SAMN11273759 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China |
| SAMN11273759 | health_condition | autoimmune_inflammatory | R1 | 0.90 | biosample_attr | Systemic lupus erythematosus |
| SAMN11273759 | health_condition_detail | Systemic lupus erythematosus | R1 | 0.90 | sample.attr.host_disease | Systemic lupus erythematosus |
| SAMN11273759 | latitude | 40.2600 | R1 | 0.90 | biosample.attribute:lat_lon | 40.26 N 116.29 E |
| SAMN11273759 | location_region | Beijing | R1 | 0.60 | biosample.attribute:lat_lon | 40.26 N 116.29 E |
| SAMN11273759 | longitude | 116.2900 | R1 | 0.90 | biosample.attribute:lat_lon | 40.26 N 116.29 E |
Sequencing
284 runs over 284 samples · mean 11.87 Gbp per run (median 11.53 Gbp, total 3,371.99 Gbp; 284 runs with a base count) · layout PAIRED 284 · platform ILLUMINA 284 · models Illumina HiSeq 3000 (284) · 92% of runs with a Sandpiper profile · first public 2020-04-26
Authors (27)
Wang Z first · Xing Y · Xu M · Chen C · Zhu Q · Chen H · Zhang Y · Chen W · Feng J · Zhang A · Ma R · Liu X · Li S · Yan Q · Xing G · Yao X · Kong X last · 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, subject_id. Share metadata
Downloads
PRJNA532888.csv.gz (7.6 KB) · parquet (81.3 KB) — all 284 samples, every field with route and confidence · PRJNA532888_determinations.csv.gz (12.8 KB) — 2,272 evidence rows