Metagenomics in diabetic foot ulcer severity, case-control
43 stool samples from adults with type 2 diabetes and active diabetic foot ulcers, comparing Wagner grades 1-3 to Wagner grade 4, identified a gut Escherichia coli-Collinsella genome signature linked to ulcer severity. machine-written summary
43 samples · 43 runs · CN · Adult · 2026 · 11.81 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 344 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 86 sample values (antibiotic exposure, subject id) · PMC13581658 |
| ○ 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 |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 43 | 100% | ||||
| country | 43 | 100% | 43 | |||
| health_condition | 43 | 100% | 43 | |||
| subject_id | 43 | 100% | 43 | |||
| antibiotic_exposure | 43 | 100% | 43 | |||
| collection_date | 43 | 100% | 43 | |||
| detailed_location | 43 | 100% | ||||
| health_condition_detail | 43 | 100% | 43 | |||
| latitude | 43 | 100% | 43 | |||
| location_locality | 43 | 100% | 43 | |||
| location_region | 43 | 100% | 43 | |||
| longitude | 43 | 100% | 43 |
- Genome-resolved gut metagenomics identifies an <i>Escherichia coli</i>-<i>Collinsella</i> signature associated with Wagner 4 gangrenous diabetic foot ulcers. 2026 PMID 42755618 PMC13581658 own_data
Archive description
Diabetic foot ulcers are a major complication of type 2 diabetes mellitus, but whether the gut microbiome captures systemic microbial features associated with advanced ulcer severity remains unclear. We performed shotgun metagenomic sequencing of stool samples from 43 patients with type 2 diabetes mellitus and active diabetic foot ulcers classified as Wagner grades 1-4. Patients with Wagner grades 1-3 were compared with patients with Wagner grade 4 gangrenous disease. De novo assembly and binning recovered 440 dereplicated metagenome-assembled genomes meeting medium-quality or high-quality thresholds. Community-level diversity and dominant-taxon composition did not clearly separate Wagner grade 4 from Wagner grades 1-3, whereas genome-level feature analysis identified a microbial signature associated with advanced disease. Random forest stability selection yielded 24 informative metagenome-assembled genomes, and intersection with covariate-adjusted MaAsLin2 analysis prioritized three shared genomes: one Escherichia coli genome enriched in Wagner grade 4 and two Collinsella genomes depleted in Wagner grade 4. Functional annotation suggested that the Wagner grade 4-enriched Escherichia coli genome carried antibiotic-resistance and virulence-factor signals and encoded respiratory metabolic capacity, whereas the two Collinsella genomes lacked detectable resistance and virulence hits and showed metabolically compact profiles. These findings support longitudinal gut metagenomic validation to determine whether this microbial signal tracks diabetic foot ulcer progression, treatment response, or recovery.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult 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 · “Genome-resolved gut metagenomics identifies an”
- body site study.description · “but whether the gut microbiome captures systemic”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN60453582 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | systemic antibiotic therapy within 4 weeks before stool collection |
| SAMN60453582 | collection_date | 2026-01 | R1 | 0.90 | biosample.attribute:collection_date | 2026-01 |
| SAMN60453582 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China: Guangxi, Nanning |
| SAMN60453582 | health_condition | type2_diabetes | R1 | 0.70 | sample.name_rule:title | Stool metagenome from T2DM_DFU_S001 |
| SAMN60453582 | health_condition_detail | T2DM | R1 | 0.70 | sample.name_rule:title | Stool metagenome from T2DM_DFU_S001 |
| SAMN60453582 | latitude | 22.7956 | R1 | 0.90 | biosample.attribute:lat_lon | 22.795565 N 108.344617 E |
| SAMN60453582 | location_locality | Nanning | R1 | 0.85 | biosample.attribute:geo_loc_name | China: Guangxi, Nanning |
| SAMN60453582 | location_region | Guangxi | R1 | 0.85 | biosample.attribute:geo_loc_name | China: Guangxi, Nanning |
| SAMN60453582 | longitude | 108.3446 | R1 | 0.90 | biosample.attribute:lat_lon | 22.795565 N 108.344617 E |
| SAMN60453582 | subject_id | SAMN60453582 | R3 | 0.75 | design.one_sample_per_subject:fulltext | This single-center cross-sectional study was approved by the Ethics Committee of the First Affiliated Hospital of Guangxi Medical University |
Sequencing
43 runs over 43 samples · mean 11.71 Gbp per run (median 11.81 Gbp, total 503.36 Gbp; 43 runs with a base count) · layout PAIRED 43 · platform ILLUMINA 43 · models Illumina NovaSeq 6000 (43) · 0% of runs with a Sandpiper profile · first public 2026-05-30
Downloads
PRJNA1471479.csv.gz (2.0 KB) · parquet (71.9 KB) — all 43 samples, every field with route and confidence · PRJNA1471479_determinations.csv.gz (3.8 KB) — 430 evidence rows