Gut Microbiota Composition in Undernourished Children Associated with Diet and Sociodemographic Factors: A Case-Control Study in Indonesia

Abstract

Malnutrition, which consists of undernutrition and overnutrition, is associated with gut microbiota composition, diet, and sociodemographic factors. Undernutrition is a nutrient deficiency that that should be identified to prevent other diseases. In this study, we evaluate the gut microbiota composition in undernourished children in association with diet and sociodemographic factors. We observed normal children (n= 20) and undernourished children (n= 20) for ten days in Lombok and Yogyakarta. Diet, sociodemographic factors, and medical records were recorded using food records, screening forms, and standard household questionnaires. Gut microbiota analysis was performed using 16S rRNA gene sequencing targeting the V3-V4 region. The result showed that the undernourished group had lower energy intake. In addition, the undernourished group had lower quality of medical records, parent knowledge, education, and exclusive breastfeeding. Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, and Verrucomicrobia were significantly different between normal and undernourished children. Based on LefSe, we determined that Akkermansia is a biomarker for undernourished children. In conclusion, diet and sociodemographic factors affect the gut microbiota composition of undernourished children.

Keywords: diet; dysbiosis; gut microbiota; sociodemographic; undernourished.

Figure 1

CONSORT flow diagram of the case–control study.

Figure 2

Ratio of Firmicutes to Bacteroidetes. Significant differences between groups were calculated using the Mann–Whitney U test (* p < 0.1).

Figure 3

The significance of gut microbiota alpha diversity was calculated using an independent t-test (* p < 0.1). (a) Chao1, species abundance between groups; (b) observed OTUs, number of species or OTUs based on the community evenness; (c) whole-tree PD, comparison of phylogenetic diversity; (d) Shannon index, species diversity between groups.

Figure 4

Beta diversity of gut microbiota composition. (a) Bray–Curtis; (b) weighted UniFrac; (c) Unweighted UniFrac.

Figure 5

Biomarker determination of gut microbiota using the taxonomic profile method of LefSe (a) and linear discriminant analysis score (b). The bar chart and cladogram show taxonomic discrimination between the two groups based on the cladogram and LDA method. Taxa with an alpha value of 0.05 and LDA score < 3.5 were considered significant.

Figure 6

Correlation between diet and gut microbiota composition generated using corrplot. The blue color indicates a positive correlation between two parameters, whereas red indicates that the two parameters are negatively correlated.

Figure 7

Principal component analysis (PCA) plot of 40 children related to calorie intake and BMI. The calorie intake (Cal) and BMI of each sample are represented by dots and color, respectively. The group sample was selected based on the four regions and circled with letters denoting the groups, namely SUB (severely undernourished children), UC (undernourished children), HC (healthy children), and SHC (super healthy children). The genus composition was averaged and graphed in the pie charts.