Association between clinical and environmental factors and the gut microbiota profiles in young South African children
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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
Nel Van Zyl K, Whitelaw AC, Hesseling AC, Seddon JA, Demers AM, Newton-Foot M
Journal
Scientific reports
Year
2021
Differences in the microbiota in populations over age and geographical locations complicate cross-study comparisons, and it is therefore essential to describe the baseline or control microbiota in each population. This includes the determination of the influence of demographic, clinical and environmental factors on the microbiota in a setting, and elucidates possible bias introduced by these factors, prior to further investigations. Little is known about the microbiota of children in South Africa after infancy. We provide a detailed description of the gut microbiota profiles of children from urban Cape Town and describe the influences of various clinical and environmental factors in different age groups during the first 5 years of life. Prevotella was the most common genus identified in the participants, and after infancy, the gut bacteria were dominated by Firmicutes and Bacteroidetes. In this setting, children exposed to antibiotics and indoor cooking fires were at the most risk for dysbiosis, showing significant losses in gut bacterial diversity.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2024-11-19
Subjects
- Location of subjects
- South Africa
- 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
- Age Age,age
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Group C (> 2 to 5 age)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Group A (0-1 age)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children within 0-1 year of age.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 66
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 12 months
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).
- centered log-ratio
- Statistical test
- ANCOM
- 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)?
- No
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-11-19
Source: Figure 5A
Description: Statistically significant taxa identified by ANCOM labelled in the Comparison between groups A (0-1 age) & C (>2 to <5 age).
Abundance in Group 1: increased abundance in Group A (0-1 age)
Revision editor(s): ToluwalaseA, Tosin
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-11-19
Source: Figure 5A
Description: Statistically significant taxa identified by ANCOM labelled in the Comparison between groups A (0-1 age) & C (>2 to <5 age).
Abundance in Group 1: decreased abundance in Group A (0-1 age)
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobacter | ||
| Lachnospiraceae bacterium NK4A136 | ||
| oscillospiraceae UCG:002oscillospiraceae UCG:002 |
Revision editor(s): ToluwalaseA, Tosin
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2024-11-19
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Group A (0-1 age)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Group B (>1 to 2 age)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with age group between > 1 to 2.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-11-19
Source: Figure 5B
Description: Statistically significant taxa identified by ANCOM labelled in the Comparison between groups A (0-1 age) & B (>1 to 2 age).
Abundance in Group 1: increased abundance in Group B (>1 to 2 age)
| NCBI | Quality Control | Links |
|---|---|---|
| Butyricicoccus | ||
| Dorea | ||
| Faecalibacterium | ||
| Haemophilus | ||
| Lachnospiraceae bacterium NK4A136 | ||
| unclassified Lachnospiraceae |
Revision editor(s): Tosin
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-11-19
Source: Figure 5B
Description: Statistically significant taxa identified by ANCOM labelled in the Comparison between groups A (0-1 age) & B (>1 to 2 age).
Abundance in Group 1: decreased abundance in Group B (>1 to 2 age)
| NCBI | Quality Control | Links |
|---|---|---|
| [Clostridium] innocuum |
Revision editor(s): Tosin
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2024-11-19
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Group B (> 1 to 2 age)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Group C (> 2 to < 5 age)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with age group between > 2 to 5.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
- Group 1 sample size Number of subjects in the case (exposed) group
- 66
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-11-19
Source: Figure 5C
Description: Statistically significant taxa identified by ANCOM labelled in the Comparison between groups B (>1 to 2 age) and C (>2 to <5 age).
Abundance in Group 1: increased abundance in Group C (> 2 to < 5 age)
| NCBI | Quality Control | Links |
|---|---|---|
| UCG:002UCG:002 | ||
| UCG:005UCG:005 |
Revision editor(s): Tosin
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-11-19
Source: Figure 5C
Description: Statistically significant taxa identified by ANCOM labelled in the Comparison between groups B (>1 to 2 age) and C (>2 to <5 age).
Abundance in Group 1: decreased abundance in Group C (> 2 to < 5 age)
| NCBI | Quality Control | Links |
|---|---|---|
| Flavonifractor | ||
| Mediterraneibacter gnavus | ||
| Thomasclavelia |
Revision editor(s): Tosin
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