Gut microbiome in V. cholerae challenge study, Baltimore
371 samples from a human Vibrio cholerae challenge study in Baltimore, USA, examining host-pathogen-microbiota interactions in gastrointestinal infection/diarrhea using an intervention design. machine-written summary
371 samples · 484 runs · US · Age unknown · 2016 · 7.96 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3,438 sample values (antibiotic exposure, collection date, country, health condition, health condition detail, latitude, location locality, location region) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC13432869 |
| ○ 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 |
longitudinal
44 of 49 people sampled more than once (366 samples; median 9, up to 13 per person) · follow-up median 6 d (max 8 mo) · median interval between samples 1 d (time from collection dates).
Each row is one person (36 shown of 44); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 348 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 | 371 | 100% | 371 | |||
| health_condition | 371 | 100% | 371 | |||
| subject_id | 371 | 100% | 371 | |||
| collection_date | 371 | 100% | 371 | |||
| detailed_location | 371 | 100% | ||||
| health_condition_detail | 371 | 100% | 371 | |||
| latitude | 371 | 100% | 371 | |||
| location_locality | 371 | 100% | 371 | |||
| location_region | 371 | 100% | 371 | |||
| longitude | 371 | 100% | 371 | |||
| antibiotic_exposure | 99 | 27% | 99 |
- gutMSNP: a comprehensive database for human gut microbial single-nucleotide polymorphisms. 2026 PMID 41359024 PMC12807719 unsure
- Fusobacterium nucleatum Enhances Intestinal Adaptation of Vibrio cholerae via Interspecies Biofilm Formation. 2026 PMID 41597730 PMC12843749 unsure
- Decoding strain level interactions between <i>Vibrio cholerae</i> and gut microbiota. 2026 PMID 42528289 PMC13432869 unsure
Archive description
This project takes advantage of challenge studies with an important human pathogen, Vibrio cholera, the etiological agent of cholera, which causes severe diarrhea in 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 age unknown by opus_adjudicated with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “Human gut microbiome with bacterial pathogen challenge”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN05971386 | antibiotic_exposure | yes | R1 | 0.85 | biosample.attribute:chem_administration | ciprofloxacin administered |
| SAMN05971381 | collection_date | 2013-09-24 | R1 | 0.90 | biosample.attribute:collection_date | 2013-09-24 |
| SAMN05971381 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Baltimore |
| SAMN05971381 | health_condition | gi_infection_or_diarrhoea | R1 | 0.90 | biosample_attr | V. cholera challenge |
| SAMN05971381 | health_condition_detail | V. cholera challenge | R1 | 0.90 | sample.attr.host_disease | V. cholera challenge |
| SAMN05971381 | latitude | 39.2885 | R1 | 0.90 | biosample.attribute:lat_lon | 39.28846263 N 76.62594594 W |
| SAMN05971381 | location_locality | Baltimore | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Baltimore |
| SAMN05971381 | location_region | Maryland | R1 | 0.60 | biosample.attribute:lat_lon | 39.28846263 N 76.62594594 W |
| SAMN05971381 | longitude | -76.6259 | R1 | 0.90 | biosample.attribute:lat_lon | 39.28846263 N 76.62594594 W |
| SAMN05971381 | subject_id | 004 | R1 | 0.85 | sample.attr.host_subject_id | 004 |
Sequencing
484 runs over 371 samples · mean 6.35 Gbp per run (median 6.98 Gbp, total 3,072.31 Gbp; 484 runs with a base count) · layout PAIRED 484 · platform ILLUMINA 484 · models Illumina HiSeq 2500 (474), Illumina HiSeq 4000 (10) · 90% of runs with a Sandpiper profile · first public 2016-12-04 – 2016-12-12
Authors (18)
Qian K first · Du M · Tan S · Ding M · Song M · Lu M · Qi C · Cheng L · Zhang X last · Chen G first · Chen J · Wang X · Guo D · Liu Z last · Li S · Zhao Q · Han Y · Zhang Z
Downloads
PRJNA352220.csv.gz (10.1 KB) · parquet (83.6 KB) — all 371 samples, every field with route and confidence · PRJNA352220_determinations.csv.gz (19.7 KB) — 3,438 evidence rows