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To the Editor: The development of gut microbiota in the early years of life is essential for immune function and protection against pathogens in humans.[1,2] Stool sample is often the first choice for analysis of the gut microbiota. The dominant five phyla observed in stool samples have been Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria, ranked in the order of abundance. However, it might be difficult to obtain the fresh stool sample from infants and young children, especially when they are diseased. In this study, we aimed to evaluate if the rectal swab sample collected from children with hand, foot, and mouth disease (HFMD) can be an alternative for microbiome study using 16S rRNA gene sequencing technology.

Use of Rectal Swab Samples for Analysis of the Intestinal Microbiome in Children