Evaluating the Effects of Rice Bran-Enriched Ready-to-Use-Therapeutic Food on Gut Microbiome in Indonesian Children With Severe Acute Malnutrition

Objectives: Background: The infant gut microbiome is a reservoir for antimicrobial resistance genes (ARGs), contributing to global antimicrobial resistance.However, risk factors for increased ARG carriage remain poorly understood.Objective: To investigate the relationship between dietary patterns and the resistome in the gut microbiome of 12-month-old infants.Methods: A cross-sectional subset of 135 infants enrolled in the Pediatric Respiratory and Enteric Viral Acquisition Longitudinal (PREVAIL) cohort with dietary information (modified Block Kids Food Frequency Questionnaire) and 12-month stool metagenomic sequencing were included.AMR++ with Mega-Res database was used to identify ARGs in the stool metagenomes.Count of ARGs was the number of unique ARGs per sample.ARG abundance was normalized using 16S copy number and gene length.The caret package was used to select a set of variables as predictors, the final included set were total sugar, dietary protein, dietary fat, dietary fiber, antibiotic use, and antiviral use.A quasi-poisson regression model was used for ARG count and a linear model was used for total normalized abundance.Results: A single outlier was excluded from the model of normalized abundance.Total dietary fat was associated with increased normalized abundance of overall ARGs (p0.0005) and an increased number of different ARGs (p0.0015).In contrast, total dietary sugar and total dietary protein (p< 0.05) were each associated with decreased normalized abundance of ARGs and tended towards a decrease in the total count of ARGs present (p< 0.10).Dietary fiber, antibiotic use, and antiviral use were not significant predictors of the abundance or number of ARGs.Conclusions: Infant diet at age 12 months is associated with infant carriage of ARGs.Total dietary fat is associated with increased ARG abundance and diversity, while total dietary sugar and protein are each associated with decreased abundance of ARGs.These findings suggest that diet during the complementary feeding period has potential to influence the resistome, and, if confirmed by work in other cohorts, may offer the potential for targeted diets to control antimicrobial resistance.