Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia
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"Study" can not be assigned to a declared number type with value 1129.PubmedParser error: Invalid PMID, please check. (PMID: 1129 Study 1129)
Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Dennis S. Nielsin, Getnet tesfaw, Nina langeland, abigail c. mapes, alemseged abdissa, ashley kates, dawd s. siraj, nasia safdar, zeleke mekonnen
Journal
Nature communications
Year
2024
Pages:
First page:
Keywords:
acute diarrhea, diarrhea, gut microbiota, Prolonged or persistent Diarrhea (ProPD)
Diarrhea claims >500,000 lives annually among children under five years of age in low- and middle-income countries. Mortality due to acute diarrhea (<7 days’ duration) is decreasing, but prolonged (7-13 days) and persistent (≥14 days of duration) diarrhea remains a massive challenge. Here, we use a case-control study to decipher if fecal gut microbiota compositional differences between Ethiopian children with acute (n=554) or prolonged/persistent (n=95) diarrhea and frequency-matched non-diarrheal controls (n=663) are linked to diarrheal etiology. We show that diarrhea cases are associated with lower bacterial diversity and enriched in Escherichia spp., Campylobacter spp., and Streptococcus spp. Further, diarrhea cases are depleted in gut commensals such as Prevotella copri, Faecalibacterium prausnitzii, and Dialister succinatiphilus, with depletion being most pronounced in prolonged/persistent cases, suggesting that prolonged duration of diarrhea is accompanied by depletion of gut commensals and that re-establishing these via e.g., microbiota-directed food supplements offer a potential treatment strategy.
Experiment 1
Needs review
Curated date: 2025/01/23
Curator:
Revision editor(s):
Subjects
- Location of subjects
- Ethiopia
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diarrhea Diarrhea,Diarrhoea,Watery stool,diarrhea
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-diarrheal controls.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Diarrhea
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The aim of our study was to decipher what differentiates the GM of children with diarrhea (AD and ProPD) from healthy controls
- Group 0 sample size Number of subjects in the control (unexposed) group
- 663
- Group 1 sample size Number of subjects in the case (exposed) group
- 650
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- DESeq2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Matched on Factors on which subjects have been matched on in a case-control study
- Matched on: "frequency" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.frequency
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- breast feeding
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Figure 4a
Description: Diarrhea cases compared with non-diarrheal controls
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia sp. | ||
| Campylobacter sp. | ||
| Streptococcus sp. | ||
| Haemophilus parainfluenzae |
Revision editor(s): Miss Lulu
Signature 2
Source: Figure 4a
Description: Diarrhea cases compared with non-diarrheal controls
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides fragilis | ||
| Prevotella corporis | ||
| Faecalibacterium prausnitzii | ||
| Dialister succinatiphilus |
Revision editor(s): Miss Lulu
Experiment 2
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Acute Diarrhea
- Group 1 sample size Number of subjects in the case (exposed) group
- 554
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- -V4
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- breast feeding, age, Confounders controlled for: "enrollment season" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.enrollment season, Confounders controlled for: "enrollment site" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.enrollment site, sex, Confounders controlled for: "WAM Index" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.WAM Index
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Figure 4b and Figure 7
Description: AD cases compared with non-diarrheal controls
Abundance in Group 1: increased abundance in Acute Diarrhea
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia sp. | ||
| Campylobacter sp. | ||
| Streptococcus sp. |
Revision editor(s): Miss Lulu
Signature 2
Source: Figure 4b and Figure 7
Description: AD cases compared with non-diarrheal controls
Abundance in Group 1: decreased abundance in Acute Diarrhea
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium prausnitzii | ||
| Prevotella corporis |
Revision editor(s): Miss Lulu
Experiment 3
Needs review
Curated date: 2025/01/23
Curator:
Revision editor(s):
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Prolonged or persistent Diarrhea (ProPD)
- Group 1 sample size Number of subjects in the case (exposed) group
- 95
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, breast feeding, sex, Confounders controlled for: "enrollment season" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.enrollment season, Confounders controlled for: "enrollment site" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.enrollment site, Confounders controlled for: "WAM Index" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.WAM Index
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Figure 4c and Figure 8
Description: ProPD cases compared with non-diarrheal controls
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia sp. | ||
| Campylobacter sp. | ||
| Streptococcus sp. |
Revision editor(s): Miss Lulu
Experiment 4
Needs review
Curated date: 2025/01/23
Curator:
Revision editor(s):
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Acute Diarrhea
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The aim of our study was to decipher what differentiates the GM of children with Prolonged or persistent diarrhea (ProPD) as compared with Acute Diarrhea
- Group 0 sample size Number of subjects in the control (unexposed) group
- 554
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 4d and Figure 9
Description: ProPD cases compared with AD cases
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Lactobacillus | ||
| Limosilactobacillus mucosae |
Revision editor(s): Miss Lulu
Signature 2
Source: Figure 4d and Figure 9
Description: ProPD cases compared with AD cases
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium prausnitzii | ||
| Akkermansia muciniphila | ||
| Anaerostipes hadrus | ||
| unclassified Coriobacteriaceae | ||
| unclassified Bacteroides |
Revision editor(s): Miss Lulu
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