Objectives : 1. To characterize the gut microbiome and 2. explore associations between dietary intake and gut microbiome composition and predicted function among children at screening for participation in a randomized controlled feeding trial in urban slums of Mumbai, India.
Young children (10-18 months old) living in urban slums of Mumbai were screened from March to November 2017 after obtaining informed consent from caregivers. Nutrient intakes from 24-hour dietary recall were analyzed as absolute intakes, % of RDA, and using the nutrient residual to adjust for energy intake. DNA extracted from rectal swabs was sequenced (16S rRNA V3-V4 region; Illumina MiSeq) and further processed using QIIME2 and PICRUSt algorithm. Linear regression was used to estimate associations between nutrient intakes (adjusted for age and sex) and measures of gut microbiome α-diversity, including Shannon Index, Chao1 estimator, observed OTUs, Proteobacteria relative abundance, Firmicutes:Bacteroidetes ratio, and predicted KEGG pathways. Statistical analysis was performed using RStudio, and SAS 9.4.
Results : A subset of 53 children with rectal swabs collected were included. Sequencing yielded 8,984,126 reads including 2,173 unique operational taxonomic units (OTUs). Mean relative abundance of Proteobacteria was 78.2%. Shannon Diversity Index was positively associated with absolute intakes of total carotenoids and beta-carotene. Children with adequate intakes of zinc and beta-carotene had a higher mean Shannon Diversity Index. The Chao1 estimator was positively associated with absolute intakes of calcium. The number of observed OTUs was positively associated with calcium and zinc intakes. The predicted gene counts for
Conclusions : The gut microbiome in this sample of young children in Mumbai was dominated by Proteobacteria, which includes many potentially pathogenic species. Dietary intakes of macro- and micronutrients were associated with measures of diversity and predicted functional pathways after adjustment for age and sex, warranting further longitudinal study of the diet’s impact on the microbiome particularly in young children.
Funding Sources : HarvestPlus