A Microbiota-Directed Food Intervention for Undernourished Children

Abstract

Background: More than 30 million children worldwide have moderate acute malnutrition. Current treatments have limited effectiveness, and much remains unknown about the pathogenesis of this condition. Children with moderate acute malnutrition have perturbed development of their gut microbiota.

Methods: In this study, we provided a microbiota-directed complementary food prototype (MDCF-2) or a ready-to-use supplementary food (RUSF) to 123 slum-dwelling Bangladeshi children with moderate acute malnutrition between the ages of 12 months and 18 months. The supplementation was given twice daily for 3 months, followed by 1 month of monitoring. We obtained weight-for-length, weight-for-age, and length-for-age z scores and mid-upper-arm circumference values at baseline and every 2 weeks during the intervention period and at 4 months. We compared the rate of change of these related phenotypes between baseline and 3 months and between baseline and 4 months. We also measured levels of 4977 proteins in plasma and 209 bacterial taxa in fecal samples.

Results: A total of 118 children (59 in each study group) completed the intervention. The rates of change in the weight-for-length and weight-for-age z scores are consistent with a benefit of MDCF-2 on growth over the course of the study, including the 1-month follow-up. Receipt of MDCF-2 was linked to the magnitude of change in levels of 70 plasma proteins and of 21 associated bacterial taxa that were positively correlated with the weight-for-length z score (P<0.001 for comparisons of both protein and bacterial taxa). These proteins included mediators of bone growth and neurodevelopment.

Conclusions: These findings provide support for MDCF-2 as a dietary supplement for young children with moderate acute malnutrition and provide insight into mechanisms by which this targeted manipulation of microbiota components may be linked to growth. (Supported by the Bill and Melinda Gates Foundation and the National Institutes of Health; ClinicalTrials.gov number, NCT04015999.).

Fig. 1:. Study design of a randomized controlled trial of MDCF-2 or RUSF supplementation in children with MAM.

(A) Study design. (B) WLZ during treatment. Best-fit linear regression lines are colored green (MDCF-2) or red (RUSF), and the lighter shaded areas around the lines indicate 95% confidence bands. The β-coefficient of +0.011 represents the weekly change in WLZ in children receiving MDCF-2 compared to those receiving RUSF. The 95% confidence interval is shown in parentheses.

Fig. 2:. Effects of Nutritional Intervention on Plasma Proteins.

(A-C) Schematic depicting the calculation of ‘β-WLZ’ for each participant (panel A), ‘Δprotein abundance’ for each participant (panel B) and the correlation between these two values (panel C). (D) Gene set enrichment analysis (GSEA) of proteins whose abundances were correlated with ponderal growth. The vertical gray line indicates q<0.05. (E-H) Gene Ontology (GO) terms enriched for by the set of WLZ-associated proteins. Shown are the correlation strengths between proteins belonging to a GO term and ponderal growth. Only proteins whose correlations with β-WLZ reached an unadjusted p<0.01 are shown. Proteins are ordered by correlation strength and colored by their p-value (transformed to a −log₁₀ scale so that decreasing values indicate less statistical significance). (I) Differential effects of MDCF-2 and RUSF on WLZ-associated proteins. Proteins are ordered by the log₂(fold-change) of the treatment effect of MDCF-2 over RUSF after three months of supplementation. GSEA was used to calculate the enrichment of proteins whose abundances were increased more by MDCF-2 compared to RUSF for the set of 70 proteins that are positively correlated with β-WLZ.

Fig. 3:. Response of the Gut Microbiota to MDCF-2 and RUSF Supplementation.

(A) Analytical scheme for linear mixed effects modeling of the relationship between WLZ and taxon (ASV) abundance during supplementation. The coefficient β₁ represents the change in WLZ for a unit change in the variance-stabilizing, transformed abundance of an ASV. A random effect for participant ID (PID) was included in the model to account for repeated measurements taken from the same individual. Bar graphs indicate β₁ (the linear model coefficients) ± SEM for each taxon that was significantly associated with WLZ. ASVs in bold-face were previously identified as ‘ecogroup’ taxa(5), while those with asterisks have previously described associations with weight gain in gnotobiotic mice harboring gut microbial communities obtained from healthy and undernourished children(10). (B) Ratio of 3-month Δ_ASV (the change in variance-stabilizing transformed ASV counts prior to and after supplementation) between MDCF-2 and RUSF treatment arms. A positive ratio indicates a greater average increase in children treated with MDCF-2. Color scheme: red bars, ASVs with significant positive associations with WLZ; blue bars, ASVs with significant negative associations with WLZ.