Gut microbiota differences in stunted and normal-lenght children aged 36-45 months in East Nusa Tenggara, Indonesia

Study information

Needs review

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

38551926

DOI Digital object identifier for electronic documents.

10.1371/journal.pone.0299349

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

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Curated date: 2025/02/22

Curator: An05hka

Revision editor(s): An05hka

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

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: decreased

Signature 1

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Curated date: 2025/02/23

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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

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Faecalibacterium
Lachnoclostridium
Veillonella

Revision editor(s): An05hka

Experiment 2

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Curated date: 2025/02/24

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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

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: decreased

Signature 1

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Curated date: 2025/02/24

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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

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Curated date: 2025/02/24

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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

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: decreased

Signature 1

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2025/02/24

Curator: An05hka

Revision editor(s): An05hka

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

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Your review change was submittedDuplicate this Experiment Add a new Signature

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Curated date: 2025/02/24

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Revision editor(s): An05hka

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