Metagenomes from travelers with diarrhea of unknown cause
Metagenomic analysis of 29 fecal samples from 23 travelers with diarrhea and 7 healthy controls, all negative for known pathogens by standard tests, to discover novel causative agents through genome assembly and characterization. machine-written summary
29 samples · 29 runs · MX, IN · Adult · 2017 · 3.88 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 87 sample values (health condition, health condition detail, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 29 sample values (antibiotic exposure) · PMC6225641 |
| ✓ Supplementary tables | 57 sample values (collection date, country) |
| – 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 | 29 | 100% | ||||
| country | 28 | 97% | 28 | |||
| health_condition | 29 | 100% | 29 | |||
| subject_id | 29 | 100% | 29 | |||
| antibiotic_exposure | 29 | 100% | 29 | |||
| collection_date | 29 | 100% | 29 | |||
| health_condition_detail | 29 | 100% | 29 |
- Visualization-assisted binning of metagenome assemblies reveals potential new pathogenic profiles in idiopathic travelers' diarrhea. 2018 PMID 30409177 PMC6225641 own_data
Archive description
Traveler's diarrhea (TD) is caused by enterotoxigenic Escherichia coli (ETEC), other pathogenic gram-negative pathogens, norovirus and some parasites. Nevertheless, standard diagnostic methods fail to identify pathogens in more than 30% of TD patients, so it is predicted that new pathogens or groups of pathogens may be causative agents of disease. A comprehensive metagenomic study of the fecal microbiomes from 23 TD patients and seven healthy travelers was performed, all of which tested negative for the known etiologic agents of TD in standard tests. Metagenomic reads were assembled and the resulting contigs were subjected to semi-manual binning to assemble independent genomes from metagenomic pools. Taxonomic and functional annotations were conducted to assist identification of putative pathogens. We extracted 560 draft genomes, 320 of which were complete enough to be enough characterized as cellular genomes and 160 of which were bacteriophage genomes... (for more see dbGaP study page.)
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.description · “fecal microbiomes from 23 TD patients”
- life stage study.description · “23 TD patients and seven healthy travelers”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN06699306 | antibiotic_exposure | no | R3 | 0.70 | paper.body.fulltext | subjects were excluded if they had taken antibiotics |
| SAMN06699306 | collection_date | 2006 | R2 | 0.85 | paper.supp.40168_2018_579_MOESM1_ESM.xlsx[Table S1!Year Sampled] | SAMN06699306: 2006 |
| SAMN06699306 | country | MX | R2 | 0.85 | paper.supp.40168_2018_579_MOESM1_ESM.xlsx[Table S1!Travel Destination] | SAMN06699306: Mexico |
| SAMN06699306 | health_condition | gi_infection_or_diarrhoea | R1 | 0.90 | biosample_attr | Diarrhea |
| SAMN06699310 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:subject_is_affected | No |
| SAMN06699306 | health_condition_detail | Diarrhea | R1 | 0.90 | sample.attr.study_disease | Diarrhea |
| SAMN06699306 | subject_id | 2004867 | R1 | 0.85 | sample.attr.gap_subject_id | 2004867 |
Sequencing
29 runs over 29 samples · mean 5.85 Gbp per run (median 3.88 Gbp, total 169.64 Gbp; 29 runs with a base count) · layout PAIRED 29 · platform ILLUMINA 29 · models NextSeq 500 (29) · 0% of runs with a Sandpiper profile · first public 2017-11-03
Authors (17)
Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last
Downloads
PRJNA382011.csv.gz (1.8 KB) · parquet (70.6 KB) — all 29 samples, every field with route and confidence · PRJNA382011_determinations.csv.gz (2.4 KB) — 173 evidence rows