Gut metagenomics, Hunner-type interstitial cystitis, Chengdu
60 fecal metagenome samples from adult and elderly participants in Chengdu, China, studying gut microbial links (notably Enterococcus avium) to Hunner-type interstitial cystitis/bladder pain syndrome. machine-written summary
60 samples · 60 runs · CN · Adult · 2025 · 6.80 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 480 sample values (age, antibiotic exposure, collection date, country, health condition, health condition detail, location locality, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 60 sample values (subject id) · PMC12868900 |
| ○ 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 59 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 | 60 | 100% | ||||
| country | 60 | 100% | 60 | |||
| health_condition | 60 | 100% | 60 | |||
| subject_id | 60 | 100% | 60 | |||
| age_at_collection_days | 60 | 100% | 60 | |||
| antibiotic_exposure | 60 | 100% | 60 | |||
| collection_date | 60 | 100% | 60 | |||
| detailed_location | 60 | 100% | ||||
| health_condition_detail | 60 | 100% | 60 | |||
| location_locality | 60 | 100% | 60 | |||
| sex | 60 | 100% | 60 |
- Multi-omics analysis identifies a microbiota-bile acid-TLR signaling axis driving bladder injury in interstitial cystitis. 2025 PMID 41457077 PMC12868900 own_data
Archive description
To achieve species-level resolution, shotgun metagenomic sequencing was also performed on fecal DNA from the same participants. Briefly, DNA was fragmented to an average size of ~400 bp for paired-end library construction using the NEXTFLE Rapid DNA-Seq kit 38. Sequencing was carried out on the Illumina NovaSeq 6000 platform (Illumina Inc., San Diego, CA, USA). Metagenomic functional annotation was performed using HUMAnN3 with the ChocoPhlAn database for human samples, and DIAMOND (v2.0.13) against the NCBI NR protein database (version 20230830) for mouse samples. Then, functional analysis of differential microorganisms in the two groups was performed. All 16S rRNA and metagenomic data were processed using the Majorbio Cloud Platform (www.majorbio.com).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.title · “fecal specimens from 30 paired human sample”
- life stage sample.attr.age · “49 (n=46/60)”
- life stage sample.attr.age · “67 (n=14/60)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN53345478 | age_at_collection_days | 24471.8 | R1 | 0.70 | sample.attr.age | 67 |
| SAMN53345478 | antibiotic_exposure | no | R1 | 0.70 | sample.name_rule:alias | alias: Health1 |
| SAMN53345478 | collection_date | 2019-01-01/2024-12-31 | R1 | 0.90 | biosample.attribute:collection_date | 2019-01-01/2024-12-31 |
| SAMN53345478 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China:Chengdu |
| SAMN53345478 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:alias | alias: Health1 |
| SAMN53345478 | health_condition_detail | Healthy women undergoing routine health examinations at our institute served as controls. | R1 | 0.70 | sample.name_rule:alias | alias: Health1 |
| SAMN53345478 | location_locality | Chengdu | R1 | 0.85 | biosample.attribute:geo_loc_name | China:Chengdu |
| SAMN53345478 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMN53345478 | subject_id | SAMN53345478 | R3 | 0.75 | design.one_sample_per_subject:fulltext | Fecal samples were collected from all participants at the time of enrollment using sterile collection containers. |
Sequencing
60 runs over 60 samples · mean 7.05 Gbp per run (median 6.80 Gbp, total 422.75 Gbp; 60 runs with a base count) · layout PAIRED 60 · platform ILLUMINA 60 · models Illumina NovaSeq 6000 (60) · 98% of runs with a Sandpiper profile · first public 2025-12-21 – 2025-12-22
Authors (18)
Peng L first · Chen JW · Chen YZ · Di XP · Lin LD · Li BY · Zhang C · Wang W · Gao XS · Ma YC · Shen SH · Li HR · Xu XF · Zeng X · Shen H · Sun Q · Jin T · Luo DY last
Downloads
PRJNA1367514.csv.gz (2.9 KB) · parquet (73.2 KB) — all 60 samples, every field with route and confidence · PRJNA1367514_determinations.csv.gz (6.0 KB) — 540 evidence rows