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Aim: This study explored the gut microbiota of children with hand, foot and mouth disease (HFMD).Methods: We enrolled 15 cases with HFMD admitted to the West China Second Hospital, Sichuan University, China, from July to September 2016 at a median age of three years. The controls were 15 healthy children of a similar age who underwent routine health examinations at the hospital during the same period. Gut microbiota was analysed using high throughput 16S ribosomal deoxyribonucleic acid sequencing.Results: The gut microbiota in the HFMD patients was distinct from the controls. Compared with the controls, the composition of gut microbiota in the HFMD cases represented a reduction of two butyrate-producing bacteria, Ruminococcus (0.73 ± 1.28 versus 7.78 ± 20.01, p = 0.026) and Roseburia (0.67 ± 1.69 versus 1.61 ± 3.27, p = 0.024) and an up-regulation of Escherichia (5.26 ± 10.50 versus 1.59 ± 5.90,p < 0.01) and Enterococcus (4.12 ± 12.49 versus 0.12 ± 0.41, p = 0.015).Conclusion: The dysbiosis of gut microbiota of the HFMD cases included a reduction of butyrate-producing bacteria and an up-regulation of inflammation-inducing bacteria. These may have impaired the intestinal biological mucosal barrier and host immune functions, promoting the invasion of the enterovirus. [ABSTRACT FROM AUTHOR]