Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice
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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
Seyoum Y, Greffeuille V, Kouadio DKD, Kuong K, Turpin W, M'Rabt R, Chochois V, Fortin S, Perignon M, Fiorentino M, Berger J, Burja K, Ponce MC, Chamnan C, Wieringa FT, Humblot C
Journal
Nature communications
Year
2024
Faecal microbiota plays a critical role in human health, but its relationship with nutritional status among schoolchildren remains under-explored. Here, in a double-blinded cluster-randomized controlled trial on 380 Cambodian schoolchildren, we characterize the impact of six months consumption of two types of rice fortified with different levels of vitamins and minerals on pre-specified outcomes. We investigate the association between the faecal microbiota (16SrRNA sequencing) and age, sex, nutritional status (underweight, stunting), micronutrient status (iron, zinc and vitamin A deficiencies, anaemia, iron deficient anaemia, hemoglobinopathy), inflammation (systemic, gut), and parasitic infection. We show that the faecal microbiota is characterised by a surprisingly high proportion of Lactobacillaceae. We discover that deficiencies in specific micronutrients, such as iron and vitamin A, correlate with particular microbiota profiles, whereas zinc deficiency shows no such association. The nutritional intervention with the two rice treatments impacts both the composition and functions predicted from compositional analysis in different ways. (ClinicalTrials.gov (Identifier: NCT01706419)).
Experiment 1
Needs review
Curated date: 2024/12/12
Curator:
Revision editor(s):
Subjects
- Location of subjects
- Cambodia
- 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
- Anemia anaemia,anemia,anemia (disease),Anemia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non anaemic
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Anaemic
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This Group includes children diagnosed with anemia with hemoglobin levels below the threshold (typically less than 11g/dl).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 304
- Group 1 sample size Number of subjects in the case (exposed) group
- 76
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
- 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
- LEfSe
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.0
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-2-7
Source: Fig. 2A
Description: Differential ASVs between the children grouped according to anaemia.
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes | ||
| [Ruminococcus] torques | ||
| Prevotella_7Prevotella_7 | ||
| PrevotellaceaeNK3B31groupPrevotellaceaeNK3B31group |
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-2-7
Source: Fig. 2A
Description: Differential ASVs between the children grouped according to their anaemic status.
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Coprobacillaceae | ||
| Faecalibacterium | ||
| Klebsiella | ||
| Lachnospira | ||
| Lachnospiraceae | ||
| Limosilactobacillus | ||
| Anaerobutyricum hallii |
Experiment 2
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No iron deficiency anaemia
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Iron deficient anaemia
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes children diagnosed with iron deficient anemia with ferritin levels below 12 µg/L in children
- Group 0 sample size Number of subjects in the control (unexposed) group
- 333
- Group 1 sample size Number of subjects in the case (exposed) group
- 47
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-2-7
Source: Fig. 2B
Description: Differential ASVs between the children grouped according to their nutritional status. Iron deficiency anaemia.
Abundance in Group 1: decreased abundance in Iron deficient anaemia
Experiment 3
Needs review
Curated date: 2024/12/15
Curator:
Revision editor(s):
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Vitamin A deficiency deficiencies, vitamin A,deficiency, vitamin A,vitamin A deficiencies,Vitamin A Deficiency,vitamin A deficiency,vitamin A deficiency (disease),Vitamin A deficiency
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Sufficient vitamin A
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vitamin A deficiency
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes children diagnosed with Vitamin A deficiency with level less than 20 micrograms per deciliter [mcg/dL]
- Group 0 sample size Number of subjects in the control (unexposed) group
- 350
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-2-7
Source: Fig. 2C
Description: Differential ASVs between the children grouped according to Vitamin A deficiency.
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Romboutsia | ||
| unidentified | ||
| Gordonibacter | ||
| Lactobacillaceae |
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-2-7
Source: Fig. 2C
Description: Differential ASVs between the children grouped according to Vitamin A deficiency
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Desulfovibrionaceae | ||
| Lachnospiraceae | ||
| Roseburia | ||
| Eubacterium ruminantium | ||
| Faecalibacterium sp. UBA1819 | ||
| [Eubacterium] siraeum |
Experiment 4
Needs review
Curated date: 2024/12/15
Curator:
Revision editor(s):
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Growth delay Delayed growth,Growth deficiency,Growth delay,Growth failure,Growth retardation,Poor growth,Retarded growth,Very poor growth,growth delay
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-stunted children
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Stunted children
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes children diagnosed with stunting with anthropometry measurement showing its prevalence at 40.0% at baseline
- Group 0 sample size Number of subjects in the control (unexposed) group
- 208
- Group 1 sample size Number of subjects in the case (exposed) group
- 172
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
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-2-7
Source: Fig. 2D
Description: Differential ASVs between the children grouped according to stunting
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Marinifilaceae | ||
| Odoribacter | ||
| Raoultibacter | ||
| Succinivibrio | ||
| Succinivibrionaceae | ||
| FamilyXIIIAD3011groupFamilyXIIIAD3011group |
Experiment 5
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Nutritional deficiency disease malnourished,malnutrition,nutritional deficiency disease,Nutritional deficiency disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Placebo
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- UR-Improved
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes children placed on the more diverse micronutrient-fortified rice (FORISCA) fortified with vitamins A, B3, and B12 as additional vitamins.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 114
- Group 1 sample size Number of subjects in the case (exposed) group
- 122
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- arcsine square-root
- Statistical test
- MaAsLin2
- 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
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-2-7
Source: Fig. 4
Description: Impact of the nutritional intervention on the taxonomic composition of the faecal microbiota of the 380 children
Abundance in Group 1: increased abundance in UR-Improved
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobacter | ||
| Blautia | ||
| Enterorhabdus | ||
| Muribaculaceae | ||
| Pediococcus | ||
| Prevotella_9Prevotella_9 | ||
| Clostridium |
Revision editor(s): Joiejoie, KateRasheed, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-2-7
Source: Fig. 4
Description: Impact of the nutritional intervention on the taxonomic composition of the faecal microbiota of the 380 children
Abundance in Group 1: decreased abundance in UR-Improved
Revision editor(s): Joiejoie, KateRasheed, WikiWorks
Experiment 6
Needs review
Curated date: 2024/12/15
Curator:
Revision editor(s):
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Inflammation inflammatory response,Inflammation,inflammation
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No inflammation
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Inflammation
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes children grouped according to systemic inflammation
- Group 0 sample size Number of subjects in the control (unexposed) group
- 240
- Group 1 sample size Number of subjects in the case (exposed) group
- 140
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
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
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-2-7
Source: S Fig. 2
Description: Differential ASVs between the children grouped according to their systemic inflammation.
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Butyricimonas | ||
| Enterococcaceae | ||
| Enterococcus | ||
| Holdemania |
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-2-7
Source: S Fig. 2
Description: Differential ASVs between the children grouped according to their systemic inflammation.
Abundance in Group 1: decreased abundance in
Revision editor(s): Joiejoie, KateRasheed, WikiWorks
Experiment 7
Needs review
Curated date: 2024/12/15
Curator:
Revision editor(s):
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Parasitic infection animal parasitic infectious disease,central nervous system parasitic infectious disease,Disease caused by parasite,disease caused by parasite,Disease caused by parasite (disorder),Disease caused by parasite, NOS,Disease, Parasitic,disease, parasitic,Diseases, Parasitic,diseases, parasitic,Ectoparasitic disease,ectoparasitic disease,Infestation,infestation,Infestation, NOS,intestinal parasitism (disorder),intestinal parasitism NOS (disorder),intestinal parasitism, unspecified,intestinal parasitism, unspecified (disorder),Parasite infestation,parasite infestation,Parasite infestation, NOS,parasitemia,parasitic animal,PARASITIC DIS,Parasitic disease,parasitic disease,Parasitic disease, NOS,Parasitic Diseases,parasitic endophthalmitis,Parasitic endophthalmitis (disorder),Parasitic endophthalmitis NOS,Parasitic endophthalmitis NOS (disorder),parasitic eye infection,Parasitic eye infection (disorder),parasitic eye infectious disease,parasitic gastrointestinal disorder,parasitic infection,Parasitic infection of lung,Parasitic infection of skin,Parasitic infection, NOS,parasitic infectious disease,Parasitic infectious disease of the central nervous system (disorder),Parasitic infectious disease, NOS,parasitic infestation of orbit,Parasitic infestation of orbit (disorder),parasitic intestinal infectious disease,parasitic liver disorder,parasitic liver infectious disease,parasitic lung infectious disease,parasitic pregnancy complication,parasitic skin disorder,parasitic skin infectious disease,Parasitic skin infestation (disorder),Parasitism,parasitism,Parasitism, NOS,Parasitosis,parasitosis,Parasitosis, NOS,psorospermiasis,Psorospermiasis (disorder),skin Infestation NOS,Parasitic infection
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No parasitic infection
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parasitic infection
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes children grouped according to parasitic infection
- Group 0 sample size Number of subjects in the control (unexposed) group
- 276
- Group 1 sample size Number of subjects in the case (exposed) group
- 104
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
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-2-7
Source: S Fig. 2B
Description: Differential ASVs between the children grouped according to parasite infection,
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Desulfovibrionaceae | ||
| Erysipelotrichaceae | ||
| Holdemanella | ||
| UCG_004UCG_004 | ||
| Weissella | ||
| Sarcina | ||
| Fastidiosipila | ||
| Oscillospiraceae |
Experiment 8
Needs review
Curated date: 2024/12/15
Curator:
Revision editor(s):
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 10-14 years old
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 6-9 years old
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes children grouped according to age (6-9 years old)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 168
- Group 1 sample size Number of subjects in the case (exposed) group
- 212
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-2-7
Source: S Fig. 2C
Description: Differential ASVs between the children grouped according to age
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Agathobacter | ||
| Butyricicoccus | ||
| Butyricicoccaceae | ||
| Anaerococcus | ||
| FamilyXIFamilyXI |
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-2-7
Source: S Fig. 2C
Description: Differential ASVs between the children grouped according to age
Abundance in Group 1: decreased abundance in
Revision editor(s): Joiejoie, KateRasheed, WikiWorks
Experiment 9
Needs review
Curated date: 2024/12/15
Curator:
Revision editor(s):
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Biological sex Biological sex,biological sex
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Girl
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Boy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes children identified on sex as a covariate feature.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 180
- Group 1 sample size Number of subjects in the case (exposed) group
- 200
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
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-2-7
Source: S Fig. 2D
Description: Differential ASVs between the children grouped according to their sex
Abundance in Group 1: increased abundance in
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-2-7
Source: S Fig. 2D
Description: Differential ASVs between the children grouped according to their sex.
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridiaceae | ||
| Eubacteriales | ||
| Gemella | ||
| Gemellaceae | ||
| Staphylococcaceae | ||
| Clostridium |
Revision editor(s): Joiejoie, KateRasheed, WikiWorks
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