Paired metagenome-metatranscriptome of CDI, Michigan adults
100 stool samples from adults in Ann Arbor, Michigan, USA (50 CDI-positive, 50 CDI-negative), analyzed with paired metagenomics and metatranscriptomics in a case-control design to study bacterial-fungal community structure and activity in C. difficile infection. machine-written summary
100 samples · 100 runs · US · Adult · 2026 · 5.03 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 700 sample values (age, collection date, country, health condition, health condition detail, location locality, location region, sex) |
| ✓ Abstract / description | 150 sample values (health condition detail, subject id) |
| ○ Full text | read; no usable statement or table · PMC11045941 |
| ○ 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 | 100 | 100% | ||||
| country | 100 | 100% | 100 | |||
| health_condition | 50 | 50% | 50 | |||
| subject_id | 100 | 100% | 100 | |||
| age_at_collection_days | 100 | 100% | 100 | |||
| collection_date | 100 | 100% | 100 | |||
| detailed_location | 100 | 100% | ||||
| health_condition_detail | 100 | 100% | 50 | 50 | ||
| location_locality | 100 | 100% | 100 | |||
| location_region | 100 | 100% | 100 | |||
| sex | 100 | 100% | 100 |
Archive description
Paired metagenomic (MG) and metatranscriptomic (MT) sequencing was performed on stool samples from 100 adults (50 CDI+, 50 CDI-) to address poorly defined functional roles of fungi and cross-kingdom interactions within the gut microbiomes of patients with Clostridioides difficile infection (CDI). Taxonomic composition, functional gene potential and expression, predicted metabolite profiles, and microbial association networks were evaluated to characterize bacterial and fungal community structure and activity. Differential abundance testing, multivariate modeling, and network analyses were applied to identify CDI-associated taxa, pathways, and trans-kingdom interactions.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.85. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.description · “stool samples from 100 adults”
- life stage study.description · “stool samples from 100 adults”
- life stage sample.attr.age · “66 (n=39/100)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN56814331 | age_at_collection_days | 21165.0 | R1 | 0.85 | sample.attr.age | 58 |
| SAMN56814331 | collection_date | 2016-03/2023-03 | R1 | 0.90 | biosample.attribute:collection_date | 2016-03/2023-03 |
| SAMN56814331 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Michigan, Ann Arbor |
| SAMN56814331 | health_condition | gi_infection_or_diarrhoea | R1 | 0.90 | biosample_attr | Clostridioides difficile infection (CDI) |
| SAMN56814331 | health_condition_detail | Clostridioides difficile infection (CDI) | R1 | 0.90 | sample.attr.disease | Clostridioides difficile infection (CDI) |
| SAMN56814381 | health_condition_detail | mixed_case_control: Case-control study with 50 CDI-positive and 50 CDI-negative subjects | R4 | 0.50 | study.description | 50 CDI+, 50 CDI- |
| SAMN56814331 | location_locality | Ann Arbor | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Michigan, Ann Arbor |
| SAMN56814331 | location_region | Michigan | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Michigan, Ann Arbor |
| SAMN56814331 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMN56814331 | subject_id | SAMN56814331 | R4 | 0.60 | design.one_sample_per_subject:description | stool samples from 100 adults (50 CDI+, 50 CDI-) |
Sequencing
100 runs over 100 samples · mean 5.35 Gbp per run (median 5.03 Gbp, total 534.74 Gbp; 100 runs with a base count) · layout PAIRED 100 · platform ELEMENT 100 · models Element AVITI (100) · 0% of runs with a Sandpiper profile · first public 2026-04-05
Authors (0)
No author record.
Downloads
PRJNA1446200.csv.gz (4.1 KB) · parquet (75.9 KB) — all 100 samples, every field with route and confidence · PRJNA1446200_determinations.csv.gz (6.5 KB) — 850 evidence rows