Gut microbiota composition differences are associated with geographic location and age in malaria-endemic regions of Rwanda
From BugSigDB
Jump to:navigation, search
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 Uniform resource identifier for web resources.
Authors
Mutoni JD, Van Hul M, Uwimana A, Petitfils C, Wong GC, Puel A, Everard A, Alexiou H, Mutesa L, Coutelier JP, Rujeni N, Cani PD
Journal
PloS one
Year
2025
Evidence suggests that a significant interplay exists between the host gut microbiota and both the transmission and severity of malaria. Therefore, we explored the association between malaria and the gut microbiota across various geographic regions, considering host's nutritional habits, helminth coinfections and age. This observational study was conducted in 3 malaria-endemic provinces of Rwanda: West, South and East. Demographic data, blood and fecal samples were collected from 169 participants (85 females and 84 males) aged between 2-78 years. We used questionnaire-derived qualitative data based on geographic regions, age, and nutrition. Malaria and soil-transmitted helminth diagnosis was assessed by microscopy. The gut microbial composition was analyzed based on bacterial 16S rRNA gene amplicon sequencing. We observed that preschool children had a significantly lower microbiota diversity compared to both school children (q = 0.027, K-Wallis) and adults (q = 0.011, K-Wallis). Unlike age, infection status (uninfected, malaria alone, soil-transmitted helminth alone or coinfection) was not significantly associated with the gut microbiota. However, using Bray-Curtis distances, we found a significantly differential gut microbial beta-diversity with a convergent distribution in the Western province compared to the other provinces (q = 0.0045, pairwise PERMANOVA). This geographic difference was not explained by any change in energy intake, protein, lipids, or carbohydrates consumption but was likely due to lower dietary fibre intake in the West compared to the South (q < 0.0001, ANOVA) and the East (q = 0.07, ANOVA). In conclusion, we have not found significant links between infection and gut microbiota. However, we showed a significant difference in the gut microbiota composition of people living in different geographic locations in Rwanda, possibly due to their nutritional habits.
Experiment 1
Subjects
- Location of subjects
- Rwanda
- 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
- Plasmodium falciparum malaria Falciparum Malaria,falciparum malaria,Falciparum malaria (disorder),Falciparum malaria [malignant tertian],falciparum malaria [malignant tertian],Malaria fever, subtertian,malaria fever, subtertian,Malaria, Falciparum,malignant tertian fever,malignant tertian fever (finding),Plasmodium falciparum malaria,Plasmodium falciparum malaria, unspecified,Plasmodium falciparum malaria, unspecified (disorder),plasmodium falciparum malaria
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- uninfected
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Infected
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with Plasmodium falciparum infection, soil-transmitted helminth infection, or co-infection
- Group 0 sample size Number of subjects in the control (unexposed) group
- 40
- Group 1 sample size Number of subjects in the case (exposed) group
- 146
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Yes
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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).
- raw counts
- Statistical test
- PERMANOVA
- 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
- age, geographic area
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, diet, geographic area
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
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Experiment 2
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Not specified
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Western Province
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Eastern Province
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants from the Eastern province of Rwanda
- 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
- 73
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- age
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, diet
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
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- 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 2B
Description: Phylum enriched in Eastern province compared to Western province, identified by ANCOM-BC
Abundance in Group 1: increased abundance in Eastern Province
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteria | ||
| Sutterellaceae | ||
| Tyzzerella | ||
| Verrucomicrobiota | ||
| Eubacterium xylanophilum | ||
| lachnospiraceae NK4B4lachnospiraceae NK4B4 |
Revision editor(s): Martha KJ
Signature 2
Source: Figure 2B
Description: Taxa depleted in Eastern province compared to Western province, identified by ANCOM-BC analysis
Abundance in Group 1: decreased abundance in Eastern Province
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Coriobacteriaceae | ||
| Erysipelotrichaceae |
Revision editor(s): Martha KJ
Experiment 3
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Southern Province
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants from the Southern province of Rwanda
- Group 1 sample size Number of subjects in the case (exposed) group
- 46
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
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- 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 2B
Description: Family enriched in Southern province compared to Western province, identified by ANCOM-BC analysis
Abundance in Group 1: increased abundance in Southern Province
| NCBI | Quality Control | Links |
|---|---|---|
| Sutterellaceae |
Revision editor(s): Martha KJ
Experiment 4
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Preschool children
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Adults
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants aged 15 years and above
- Group 0 sample size Number of subjects in the control (unexposed) group
- 37
- Group 1 sample size Number of subjects in the case (exposed) group
- 96
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- yes
Lab analysis
Statistical Analysis
- Statistical test
- ANCOM
- Kruskall-Wallis
- PERMANOVA
- Matched on Factors on which subjects have been matched on in a case-control study
- geographic area
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- diet, geographic area
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
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 4
Description: Taxa enriched in adults compared to preschool children, identified by ANCOM-BC analysis
Abundance in Group 1: increased abundance in Adults
Revision editor(s): Martha KJ
Signature 2
Source: Figure 4
Description: Taxa depleted in adults compared to preschool children, identified by ANCOM-BC analysis
Abundance in Group 1: decreased abundance in Adults
| NCBI | Quality Control | Links |
|---|---|---|
| CampilobacterotaCampilobacterota | ||
| Campylobacteraceae | ||
| Campylobacter |
Revision editor(s): Martha KJ
Experiment 5
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- School children
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children aged 5-14 years
- Group 1 sample size Number of subjects in the case (exposed) group
- 36
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
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Figure 4
Description: Genera enriched in school children compared to preschool children, identified by ANCOM-BC analysis
Abundance in Group 1: increased abundance in School children
| NCBI | Quality Control | Links |
|---|---|---|
| uncultured Lachnospiraceae bacterium | ||
| Moryella |
Revision editor(s): Martha KJ
Experiment 6
40460079/Experiment 6
Retrieved from "https://bugsigdb.org/w/index.php?title=40460079&oldid=210221"
