Gut microbiota differences in stunted and normal-lenght children aged 36-45 months in East Nusa Tenggara, Indonesia
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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
Surono IS, Popov I, Verbruggen S, Verhoeven J, Kusumo PD, Venema K
Journal
PloS one
Year
2024
The role of the gut microbiota in energy metabolism of the host has been established, both in overweight/obesity, as well as in undernutrition/stunting. Dysbiosis of the gut microbiota may predispose to stunting. The aim of this study was to compare the gut microbiota composition of stunted Indonesian children and non-stunted children between 36 and 45 months from two sites on the East Nusa Tenggara (ENT) islands. Fecal samples were collected from 100 stunted children and 100 non-stunted children in Kupang and North Kodi. The gut microbiota composition was determined by sequencing amplicons of the V3-V4 region of the 16S rRNA gene. Moreover, fecal SCFA concentrations were analyzed. The microbiota composition was correlated to anthropometric parameters and fecal metabolites. The phyla Bacteroidetes (Bacteroidota; q = 0.014) and Cyanobacteria (q = 0.049) were significantly higher in stunted children. Three taxa at genus levels were consistently significantly higher in stunted children at both sampling sites, namely Lachnoclostridium, Faecalibacterium and Veillonella (q < 7 * 10-4). These and 9 other taxa positively correlated to the z-score length-for-age (zlen), while 11 taxa negatively correlated with zlen. Several taxa also correlated with sanitary parameters, some of which were also significantly different between the two groups. All three fecal SCFA concentrations (acetate, propionate and butyrate) and their total were lower in stunted children compared to non-stunted children, although not significant for butyrate, indicating lower energy-extraction by the gut microbiota. Also, since SCFA have been shown to be involved in gut barrier function, barrier integrity may be affected in the stunted children. It remains to be seen if the three taxa are involved in stunting, or are changed due to e.g. differences in diet, hygiene status, or other factors. The observed differences in this study do not agree with our previous observations in children on Java, Indonesia. There are differences in infrastructure facilities such as clean water and sanitation on ENT and Java, which may contribute to the differences observed. The role of the gut microbiota in stunting therefore requires more in depth studies. Trial registration: the trial was registered at ClinicalTrials.gov with identifier number NCT05119218.
Experiment 1
Subjects
- Location of subjects
- Indonesia
- 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
- Short stature Decreased body height,Height less than 3rd percentile,Short stature,Small stature,Stature below 3rd percentile,short stature
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal Length children
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Stunted Length children
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Stunted length children aged 36–45 months
- Group 0 sample size Number of subjects in the control (unexposed) group
- 100
- Group 1 sample size Number of subjects in the case (exposed) group
- 100
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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
- Kruskall-Wallis
- 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
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 4.
Description: Boxplots of the 3 taxa at genus level that were significantly different between non-stunted and stunted children.
Abundance in Group 1: increased abundance in Stunted Length children
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Lachnoclostridium | ||
| Veillonella |
Revision editor(s): An05hka
Experiment 2
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal Length children in Kupang
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Stunted Length children in Kupang
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Stunted length children aged 36–45 months from Kupang
- Group 0 sample size Number of subjects in the control (unexposed) group
- 50
- Group 1 sample size Number of subjects in the case (exposed) group
- 50
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 4.
Description: Boxplots of the 3 taxa at genus level that were significantly different (Kruskal-Wallis analysis, with Benjamini-Hochberg FDR correction) between non-stunted and stunted children of Kupang.
Abundance in Group 1: increased abundance in Stunted Length children in Kupang
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Veillonella | ||
| Lachnoclostridium |
Revision editor(s): An05hka
Experiment 3
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal Length children from North Kodi
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Stunted Length children from North Kodi
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Stunted length children aged 36–45 months from North Kodi
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Figure 4.
Description: Boxplots of the 3 taxa at genus level that were significantly different (Kruskal-Wallis analysis, with Benjamini-Hochberg FDR correction) between non-stunted and stunted children from North Kodi
Abundance in Group 1: increased abundance in Stunted Length children from North Kodi
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonella | ||
| Faecalibacterium | ||
| Lachnoclostridium |
Revision editor(s): An05hka
Experiment 4
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal Length children
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Stunted Length children
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Stunted length children aged 36–45 months
- Group 0 sample size Number of subjects in the control (unexposed) group
- 100
- Group 1 sample size Number of subjects in the case (exposed) group
- 100
Lab analysis
Statistical Analysis
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Signature 1
Source: Table 3.
Description: Gut microbiota composition at the phylum level
Abundance in Group 1: increased abundance in Stunted Length children
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidia | ||
| Cyanobacteriota |
Revision editor(s): An05hka
Experiment 5
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Body weight weight,Body weight,body weight
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- low Weight
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Weight
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with high weight aged 36-45 months
Lab analysis
Statistical Analysis
- Statistical test
- Spearman Correlation
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Signature 2
Source: Figure 6 A , weight
Description: Heatmap of the taxa at genus level that were different (q < 0.05) when correlated by Spearman correlation analysis to the weight. Blue: Positive correlation; red: Negative correlation
Abundance in Group 1: decreased abundance in High Weight
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcaceae D5 unculturedRuminococcaceae D5 uncultured |
Revision editor(s): An05hka
Experiment 6
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Body height height,Body height,body height
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Height
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Height
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with high Height aged 36-45 months
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 6A. ,height
Description: Heatmap of the taxa at genus level that were different (q < 0.05) when correlated by Spearman correlation analysis to the Height. Blue: Positive correlation; red: Negative correlation.
Abundance in Group 1: increased abundance in High Height
Revision editor(s): An05hka
Signature 2
Source: Figure 6A. ,height
Description: Heatmap of the taxa at genus level that were different (q < 0.05) when correlated by Spearman correlation analysis to the Height. Positive correlation; red: Negative correlation
Abundance in Group 1: decreased abundance in High Height
Revision editor(s): An05hka
Experiment 7
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Body mass index BMI,Quetelet's Index,Body mass index,body mass index
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low BMI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High BMI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with high Body Mass Index (BMI) aged 36-45 months
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Signature 1
Source: Figure 6A., BMI
Description: Heatmap of the taxa at genus level that were different (q < 0.05) when correlated by Spearman correlation analysis to the BMI. Positive correlation; red: Negative correlation
Abundance in Group 1: increased abundance in High BMI
Revision editor(s): An05hka
Signature 2
Source: Figure 6A., BMI
Description: Heatmap of the taxa at genus level that were different (q < 0.05) when correlated by Spearman correlation analysis to the BMI. Positive correlation; red: Negative correlation
Abundance in Group 1: decreased abundance in High BMI
Revision editor(s): An05hka
Experiment 8
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Body height height,Body height,body height
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Height
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Height
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with high Height aged 36-45 months.
- Data was Z-score Transformed
Lab analysis
Statistical Analysis
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