Gut microbiome in adults with ETEC challenge, Baltimore, USA
109 samples from adults with GI infection/diarrhoea in Baltimore, USA, collected during an enterotoxigenic E. coli human challenge intervention study examining host-pathogen-microbiota interactions. machine-written summary
109 samples · 908 runs · US · Adult · 2016 · 14.95 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 953 sample values (antibiotic exposure, collection date, country, health condition, health condition detail, intervention, latitude, location locality) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 112 sample values (health condition, health condition detail) · PMC12807719, PMC8342411 |
| ✓ Supplementary tables | 4 sample values (timepoint) |
| – 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 |
Other administered intervention (see intervention_detail) · population gi_infection_or_diarrhoea · Enterotoxigenic E. coli human challenge study
“challenge studies with an important human pathogen, enterotoxigenic Escherichia coli” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
6 of 8 people sampled more than once (106 samples; median 18, up to 21 per person) · follow-up median 29 d (max 29 d) · median interval between samples 1 d (time from collection dates). Schedule stated by the source: “Stool samples collected at multiple timepoints (Day 1, Day 2, Day 6, Day 10) per subject during ETEC challenge study; 8 subjects with repeated samples, 6 subjects with >1 sample.”; stated follow-up 10 d.
Each row is one person (6 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 102 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 | 109 | 100% | ||||
| country | 109 | 100% | 109 | |||
| health_condition | 109 | 100% | 53 | 56 | ||
| subject_id | 108 | 99% | 108 | |||
| collection_date | 109 | 100% | 109 | |||
| detailed_location | 109 | 100% | ||||
| health_condition_detail | 109 | 100% | 53 | 56 | ||
| latitude | 109 | 100% | 109 | |||
| location_locality | 109 | 100% | 109 | |||
| location_region | 109 | 100% | 109 | |||
| longitude | 109 | 100% | 109 | |||
| antibiotic_exposure | 43 | 39% | 43 | |||
| intervention | 42 | 39% | 42 | |||
| timepoint_label | 4 | 4% | 4 |
- Evaluation of a high-throughput, cost-effective Illumina library preparation kit. 2021 PMID 34354114 PMC8342411 own_data
- gutMSNP: a comprehensive database for human gut microbial single-nucleotide polymorphisms. 2026 PMID 41359024 PMC12807719 unsure
Archive description
This project takes advantage of challenge studies with an important human pathogen, enterotoxigenic Escherichia coli, the etiological agent of severe diarrhea in the developed countries and traveler’s diarrhea in individuals from developed countries. The goal of this study is to understand the dynamic interactions between the host, pathogen and microbiota and how these interactions play a role in determining the pathogen population in the host, the development of an immune response, and the diversity and ecology of the microbiota. The project uses a combination of genomic, transcriptomic and metagenomic technologies together with human challenge studies to generate new insights into the interaction of host, pathogen, and microbiota.
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 · “Human gut microbiome with bacterial”
- body site external_curation.infant_catalog · “body_site_call gut”
- 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 |
|---|---|---|---|---|---|---|
| SAMN05545000 | antibiotic_exposure | yes | R1 | 0.85 | biosample.attribute:chem_administration | ciprofloxacin administered |
| SAMN05544800 | collection_date | 2014-06-10 | R1 | 0.90 | biosample.attribute:collection_date | 2014-06-10 |
| SAMN05544800 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:Baltimore |
| SAMN05544993 | health_condition | gi_infection_or_diarrhoea | R1 | 0.70 | biosample_attr | ETEC H10407 challenge |
| SAMN05544800 | health_condition | gi_infection_or_diarrhoea | R3 | 0.60 | paper.fulltext.results | stool metagenomic samples acquired from an enterotoxigenic E. coli (ETEC) infected individual |
| SAMN05544993 | health_condition_detail | ETEC H10407 challenge | R1 | 0.90 | sample.attr.host_disease | ETEC H10407 challenge |
| SAMN05544800 | health_condition_detail | infected individual with an enterotoxigenic E. coli (ETEC) infection | R3 | 0.60 | paper.fulltext.results | stool metagenomic samples acquired from an enterotoxigenic E. coli (ETEC) infected individual |
| SAMN05545000 | intervention | antibiotic | R1 | 0.85 | biosample.attribute:chem_administration | ciprofloxacin administered |
| SAMN05544800 | latitude | 39.2885 | R1 | 0.90 | biosample.attribute:lat_lon | 39.28846263 N 76.62594594 W |
| SAMN05544800 | location_locality | Baltimore | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Baltimore |
| SAMN05544800 | location_region | Maryland | R1 | 0.60 | biosample.attribute:lat_lon | 39.28846263 N 76.62594594 W |
| SAMN05544800 | longitude | -76.6259 | R1 | 0.90 | biosample.attribute:lat_lon | 39.28846263 N 76.62594594 W |
| SAMN05544989 | subject_id | 001 | R1 | 0.85 | sample.attr.host_subject_id | 001 |
| SAMN05545049 | timepoint_label | Day 10 | R2 | 0.85 | paper.supp.41598_2021_94911_MOESM1_ESM.xlsx[TableS1!strain/sample] | Day 10 |
Sequencing
908 runs over 109 samples · mean 1.75 Gbp per run (median 0.79 Gbp, total 1,591.53 Gbp; 908 runs with a base count) · layout PAIRED 908 · platform ILLUMINA 908 · models Illumina HiSeq 2500 (908) · 19% of runs with a Sandpiper profile · first public 2016-10-25 – 2020-02-07
Authors (19)
Tvedte ES first · Michalski J · Cheng S · Patkus RS · Tallon LJ · Sadzewicz L · Bruno VM · Silva JC · Rasko DA · Dunning Hotopp JC last · Qian K first · Du M · Tan S · Ding M · Song M · Lu M · Qi C · Cheng L · Zhang X last
Downloads
PRJNA338184.csv.gz (4.0 KB) · parquet (75.6 KB) — all 109 samples, every field with route and confidence · PRJNA338184_determinations.csv.gz (7.8 KB) — 1,069 evidence rows