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PRJNA976726 SRP445612

Longitudinal cholera patient stool metagenomes, Bangladesh

Cholera patient metagenomes

344 stool metagenome samples from diarrheal disease patients in Bangladesh, collected at hospital admission to study Vibrio cholerae, phages, and gut microbiome taxa alongside antibiotic exposure, in a longitudinal design. machine-written summary

344 samples · 344 runs · BD · Age unknown · 2023 · 6.85 Gbp / sample

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Sources
✓Sequence archive 2,408○Abstract / description○Full text○Supplementary tables–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave
✓ Sequence archive2,408 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude)
○ Abstract / descriptionread; no usable statement
○ Full textread; no usable statement or table · PMC12843749, PMC13432869
○ Supplementary tablesfiles read; no table could be matched to the samples
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet · share metadata
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
1 sampling locations · 1 country
Age
unknown344
Condition
gi_infection_or_diarrhoea344
Country
BD344
Body site
primary344
Collected 2018–2019
2018: 333 samples2019: 11 samples20182019
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)all projects, 0.03–0.1 Gbp: 17,066 samples (3 %)all projects, 0.1–0.3 Gbp: 29,179 samples (5 %)all projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 16 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 57 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 220 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 51 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 6.85 Gbp per sample0130Gbp
Community composition
Vibrio 24.3%Escherichia 21.5%Streptococcus 11.6%Bifidobacterium 4.9%Prevotella 4.4%Campylobacter_D 2.5%Brachyspira 1.8%Enterococcus_B 1.6%Campylobacter 1.6%ECMA0423 1.4%Alloprevotella 1.4%Fusobacterium_A 1.4%not assigned to a genus 5.3%other genera 16.5%

Genera, mean relative abundance over 314 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category0 0%
country344 100%344
health_condition344 100%344
subject_id0 0%
collection_date344 100%344
detailed_location344 100%
health_condition_detail344 100%344
latitude344 100%344
location_region344 100%344
longitude344 100%344
Papers (2)
  • 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
Details
Archive description

To understand the roles of antibiotics and lytic phages on Vibrio cholerae infections and disease outcomes, we conducted a national prospective longitudinal study in the cholera endemic setting of Bangladesh. Stool samples were collected at hospital admission from diarrheal disease patients and screened for Vibrio cholerae or V. cholerae phage. Among positive samples, we sequenced shotgun metagenomes to quantify the relative abundances of V. cholerae, phages, and gut microbiome taxa, while accounting for antibiotic exposure determined by mass spectrometry.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.85. Assay shotgun_dna.

  • host run.host_tax_id · “9606”
  • host run.scientific_name · “human feces metagenome”
  • body site study.description · “Stool samples were collected”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN35522281collection_date2018-03-14R10.90biosample.attribute:collection_date2018-03-14
SAMN35522281countryBDR10.90sample.attr.geo_loc_nameBangladesh
SAMN35522281health_conditiongi_infection_or_diarrhoeaR10.85biosample.attribute:isolation_sourcestool
SAMN35522281health_condition_detailstoolR10.85biosample.attribute:isolation_sourcestool
SAMN35522281latitude23.6850R10.90biosample.attribute:lat_lon23.685 N 90.3563 E
SAMN35522281location_regionDhakaR10.60biosample.attribute:lat_lon23.685 N 90.3563 E
SAMN35522281longitude90.3563R10.90biosample.attribute:lat_lon23.685 N 90.3563 E
Sequencing

344 runs over 344 samples · mean 6.48 Gbp per run (median 6.85 Gbp, total 2,228.15 Gbp; 344 runs with a base count) · layout PAIRED 344 · platform ILLUMINA 344 · models Illumina NovaSeq 6000 (344) · 92% of runs with a Sandpiper profile · first public 2023-06-27

Authors (9)

Chen G first · Chen J · Wang X · Guo D · Liu Z last · Li S · Zhao Q · Han Y · Zhang Z

Help complete this project

2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata

Downloads

PRJNA976726.csv.gz (9.3 KB) · parquet (83.2 KB) — all 344 samples, every field with route and confidence · PRJNA976726_determinations.csv.gz (14.6 KB) — 2,408 evidence rows

Samples (344 · every field this project has values for · hover a cell for its source)
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