Diarrhea outbreak fecal metagenomes, Germany, case-control
44 fecal samples from patients during the 2011 German STEC O104:H4 diarrhea outbreak, including STEC-positive cases with varying clinical severity and a few patients with other infections (Campylobacter jejuni, C. difficile, Salmonella); case-control design. machine-written summary
44 samples · 53 runs · DE · Age unknown · 2013 · 1.01 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 88 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC12468353, PMC4164323, PMC4992282, PMC5607848, PMC9817263 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 88 sample values (health condition, health condition detail) · from curatedMetagenomicData 3 (cMD 3), GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 33 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 | 44 | 100% | 44 | |||
| health_condition | 44 | 100% | 44 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 44 | 100% | 44 | |||
| health_condition_detail | 44 | 100% | 44 |
- A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. 2013 PMID 23571589 own_data
- PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples. 2014 PMID 25225611 PMC4164323 own_data
- A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes. 2016 PMID 27542753 PMC4992282 own_data
- DESMAN: a new tool for de novo extraction of strains from metagenomes. 2017 PMID 28934976 PMC5607848 own_data
- MetaBinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities. 2023 PMID 36609515 PMC9817263 own_data
6 more
- A Graph Contrastive Learning Method for Enhancing Genome Recovery in Complex Microbial Communities. 2025 PMID 41008047 PMC12468353
- Metagenomic growth rate inferences of strains in situ. 2020 PMID 32494636 PMC7176420
- The human gut archaeome: identification of diverse haloarchaea in Korean subjects. 2020 PMID 32753050 PMC7409454
- Phage Cocktails Constrain the Growth of Enterococcus. 2022 PMID 35762793 PMC9426582
- High-resolution strain-level microbiome composition analysis from short reads. 2023 PMID 37587527 PMC10433603
- Effective binning of metagenomic contigs using contrastive multi-view representation learning. 2024 PMID 38233391 PMC10794208
Archive description
Design, Setting and Patients Forty-five samples were selected from a set of fecal specimens obtained from patients with diarrhea during the 2011 outbreak of STEC O104:H4 in Germany. Samples were chosen to represent STEC-positive patients with a range of clinical conditions and colony counts together with a small number of patients with other infections (Campylobacter jejnuni, Clostridium difficile and Salmonella enterica). Samples were subjected to high-throughput sequencing on the Illumina MiSeq and HiSeq 2500, followed by bioinformatics analysis.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.66. Assay shotgun_dna.
- host run.scientific_name · “human metagenome”
- body site study.description · “fecal specimens obtained from patients with diarrhea”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA1877322 | collection_date | 2011 | R1 | 0.90 | biosample.attribute:collection_date | 2011 |
| SAMEA1877322 | country | DE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Germany |
| SAMEA1877322 | health_condition | other_infection | R2 | 0.75 | external.cmd source | disease: Escherichia coli Infection |
| SAMEA1877332 | health_condition | gi_infection_or_diarrhoea | R2 | 0.75 | external.gmrepo source | phenotype: Diarrhea |
| SAMEA1877322 | health_condition_detail | Escherichia coli Infection | R2 | 0.75 | external.cmd source | disease: Escherichia coli Infection |
| SAMEA1877332 | health_condition_detail | Diarrhea | R2 | 0.75 | external.gmrepo source | phenotype: Diarrhea |
Sequencing
53 runs over 44 samples · mean 1.25 Gbp per run (median 0.97 Gbp, total 66.17 Gbp; 53 runs with a base count) · layout PAIRED 53 · platform ILLUMINA 53 · models Illumina HiSeq 2500 (43), Illumina MiSeq (10) · 70% of runs with a Sandpiper profile · first public 2013-04-16 – 2013-04-17
Authors (24)
Loman NJ first · Constantinidou C · Christner M · Rohde H · Chan JZ · Quick J · Weir JC · Quince C · Smith GP · Betley JR · Aepfelbacher M · Pallen MJ last · Wang Z first · Huang P · You R · Sun F · Zhu S last · Liao H first · Ji Y · Sun Y last · Han H · Liu W · Wei G first · Liu Y last
Downloads
PRJEB1775.csv.gz (1.9 KB) · parquet (70.3 KB) — all 44 samples, every field with route and confidence · PRJEB1775_determinations.csv.gz (2.4 KB) — 176 evidence rows