Gut microbiome in C. difficile infection, Hangzhou, China
53 fecal metagenome samples from patients with gastrointestinal infection or diarrhoea in Hangzhou, China, characterizing the gut microbiome in Clostridioides difficile infection. machine-written summary
53 samples · 53 runs · CN · Age unknown · 2023 · 13.47 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 424 sample values (collection date, country, latitude, location locality, location region, longitude, subject id, timepoint) |
| – Abstract / description | no abstract or project description |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| ✓ External resources | 106 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
14 of 14 people sampled more than once (53 samples; median 4, up to 7 per person) · follow-up median 31 d (max 31 d) · median interval between samples 31 d (time from collection months (month precision)). Schedule stated by the source: “Same subject_id sampled at multiple dated timepoints tracking CDN->CDCp and PRECDI->ONCDI->POSTCDI disease stages, no fixed day offsets stated” (time origin: other).
Each row is one person (9 shown of 14); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 50 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 | 53 | 100% | 53 | |||
| health_condition | 53 | 100% | 53 | |||
| subject_id | 53 | 100% | 53 | |||
| collection_date | 53 | 100% | 53 | |||
| detailed_location | 53 | 100% | ||||
| health_condition_detail | 53 | 100% | 53 | |||
| latitude | 53 | 100% | 53 | |||
| location_locality | 53 | 100% | 53 | |||
| location_region | 53 | 100% | 53 | |||
| longitude | 53 | 100% | 53 | |||
| timepoint_label | 53 | 100% | 53 |
- Characterization and dynamics of intestinal microbiota in patients with Clostridioides difficile colonization and infection. 2024 PMID 38857786 own_data
Archive description
Characterization of gut microbiome in patients with Clostridioides difficile infection
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “fecal metagenome Raw sequence reads”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN27401454 | collection_date | 2019-03 | R1 | 0.90 | biosample.attribute:collection_date | 2019-03 |
| SAMN27401454 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China: Hangzhou |
| SAMN27401454 | health_condition | gi_infection_or_diarrhoea | R2 | 0.75 | external.gmrepo source | phenotype: Clostridium Infections |
| SAMN27401454 | health_condition_detail | Clostridium Infections | R2 | 0.75 | external.gmrepo source | phenotype: Clostridium Infections |
| SAMN27401454 | latitude | 30.2800 | R1 | 0.90 | biosample.attribute:lat_lon | 30.28 N 120.15 E |
| SAMN27401454 | location_locality | Hangzhou | R1 | 0.85 | biosample.attribute:geo_loc_name | China: Hangzhou |
| SAMN27401454 | location_region | Zhejiang Sheng | R1 | 0.60 | biosample.attribute:lat_lon | 30.28 N 120.15 E |
| SAMN27401454 | longitude | 120.1500 | R1 | 0.90 | biosample.attribute:lat_lon | 30.28 N 120.15 E |
| SAMN27401454 | subject_id | BJF | R1 | 0.70 | sample.name_rule:sample_alias | BJF190322 |
| SAMN27401454 | timepoint_label | 190322 | R1 | 0.70 | sample.name_rule:sample_alias | BJF190322 |
Sequencing
53 runs over 53 samples · mean 13.90 Gbp per run (median 13.47 Gbp, total 736.95 Gbp; 53 runs with a base count) · layout PAIRED 53 · platform ILLUMINA 53 · models Illumina NovaSeq 6000 (53) · 94% of runs with a Sandpiper profile · first public 2023-07-30
Authors (0)
No author record.
Downloads
PRJNA824338.csv.gz (2.5 KB) · parquet (72.5 KB) — all 53 samples, every field with route and confidence · PRJNA824338_determinations.csv.gz (4.8 KB) — 530 evidence rows