Objectives: Maturation of the gut microbiota has been shown to influence childhood growth while alterations in microbiota composition are proposed to be causally related to the development of overweight and obesity. The objective of this study is to explore the association between microbiota profile, body size and body composition in young children. Methods: Faecal microbiota was examined by 16S rRNA gene sequencing while body composition was assessed using the deuterium oxide dilution technique in a cohort of 37 well-nourished 2 to 3 year old Australian children. Results: Microbiota composition (weighted UniFrac distance) was shown to be significantly associated with FFMI (Fat Free Mass Index) Z score (p = 0.027, adonis) in boys but not girls. In boys, FFMI Z score was significantly correlated with the relative abundance of an OTU belonging to the Ruminococcaceae family (Rho = 0.822, p
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