Gut microbiota succession after cholera/ETEC diarrhea, Bangladesh
Longitudinal cohort of 49 gut metagenome samples from Bangladesh, comparing individuals with acute secretory diarrhea (V. cholerae or ETEC infection, n=40) to healthy controls (n=9), tracking microbial community succession during recovery. machine-written summary
49 samples · 49 runs · BD · Infant / toddler · 2015 · 0.61 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 49 sample values (country) |
| ✓ Abstract / description | 2 sample values (health condition) |
| ○ Full text | read; no usable statement or table · PMC9512645 |
| ✓ Supplementary tables | 98 sample values (subject id, timepoint) |
| ✓ External resources | 94 sample values (health condition, health condition detail) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
9 of 28 people sampled more than once (30 samples; median 3, up to 4 per person) · follow-up median 27 d (max 30 d) · median interval between samples 14 d (time from timepoint labels). Schedule stated by the source: “Longitudinal cohort tracking gut microbial succession during recovery from acute secretory diarrhea (cholera or ETEC) over time after infection.” (time origin: diagnosis).
Each row is one person (9 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 38 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 | 49 | 100% | 49 | |||
| health_condition | 49 | 100% | 47 | 2 | ||
| subject_id | 49 | 100% | 49 | |||
| timepoint_label | 49 | 100% | 49 | |||
| health_condition_detail | 47 | 96% | 47 |
- Gut microbe metabolism of small molecules supports human development across the early stages of life. PMID 36177457 PMC9512645 curated
- Exploring the vitamin biosynthesis landscape of the human gut microbiota. PMID 39287373 PMC11494892 curated
Archive description
Disability after childhood diarrhea is an important burden on global productivity. Recent studies suggest that gut bacterial communities influence how humans recover from infectious diarrhea, but we still lack extensive data and mechanistic hypotheses for how these communities respond to diarrheal disease and its treatment. Here, we report that after V. cholerae infection, human gut microbiota undergo an orderly and reproducible succession featuring transient reversals in relative levels of enteric Bacteroides and Prevotella. Elements of this succession may be a common feature in microbiota recovery from acute secretory diarrhea, as we observed similar successional dynamics after enterotoxigenic Escherichia coli (ETEC) infection. Our metagenomic analyses suggest multiple mechanisms driving microbial succession after cholera, including bacterial dispersal properties, changing enteric oxygen and carbohydrate levels, and phage dynamics. Thus, gut microbiota recovery after cholera may be predictable at the level of community structure, but driven by a complex set of temporally varying ecological processes. Our findings suggest opportunities for diagnostics and therapies targeting the gut microbiota in humans recovering from infectious diarrhea.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “Gut microbial succession follows”
- body site study.description · “studies suggest that gut bacterial communities influence”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “Disability after childhood diarrhea is an”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA3360657 | country | BD | R1 | 0.90 | biosample_attr | Bangladesh |
| SAMEA3360657 | health_condition | gi_infection_or_diarrhoea | R2 | 0.75 | external.cmd source | disease: Diarrhea;Cholera |
| SAMEA3360685 | health_condition | gi_infection_or_diarrhoea | R4 | 0.45 | study.description | after V. cholerae infection, human gut microbiota |
| SAMEA3360657 | health_condition_detail | Diarrhea;Cholera | R2 | 0.75 | external.cmd source | disease: Diarrhea;Cholera |
| SAMEA3360657 | subject_id | 1-C-0 | R2 | 0.85 | paper.supp.mbo002152307st2.xlsx[Table S2!Cohort+Household+Subject/Contact] | LD-Run1-01 | Cohort 1 | Household C | Subject/Contact 0 | day 1 |
| SAMEA3360657 | timepoint_label | day 1 | R2 | 0.85 | paper.supp.mbo002152307st2.xlsx[Table S2!Sample day (dpp)] | LD-Run1-01 | Cohort 1 | Household C | Subject/Contact 0 | day 1 |
Sequencing
49 runs over 49 samples · mean 0.88 Gbp per run (median 0.61 Gbp, total 43.26 Gbp; 49 runs with a base count) · layout PAIRED 49 · platform ILLUMINA 49 · models Illumina HiSeq 2500 (37), Illumina HiSeq 2000 (12) · 78% of runs with a Sandpiper profile · first public 2015-04-29
Authors (9)
Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last · van Sinderen D
Downloads
PRJEB9150.csv.gz (2.3 KB) · parquet (71.4 KB) — all 49 samples, every field with route and confidence · PRJEB9150_determinations.csv.gz (3.4 KB) — 243 evidence rows