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Idiopathic short stature (ISS) accounts for more than 70% of childhood short stature cases, with an undefined etiology and pathogenesis, leading to limited treatment. However, recent studies have shown that intestinal microbiota may be associated with ISS. This study aimed to characterize the intestinal microbiota in children with ISS, effect of treatment with growth hormones, and association between specific bacterial species and ISS. This study enrolled 55 children, comprising 40 diagnosed with ISS at Jinhua Hospital, Zhejiang University, and 15 healthy controls. The subjects with ISS were divided into the untreated ISS group (UISS group, 22 children who had not been treated with recombinant human growth hormone [rhGH]), treated ISS group (TISS group, 18 children treated with rhGH for 1 year), and control group (NC group, 15 healthy children). High-throughput sequencing was used to determine the intestinal microbiota characteristics. Higher abundances of Bacteroides, Prevotella, Alistipes, Parabacteroides, Agathobacter and Roseburia were found in the UISS and TISS groups than in the control group, whereas Bifidobacterium, Subdoligranulum, and Romboutsia were less abundant. The composition of intestinal microbiota in the UISS and TISS groups was almost identical, except for Prevotella. The TISS group had significantly lower levels of Prevotella than did the UISS group, which were closer to those of the NC group. Receiver operating characteristic curve analysis revealed that the abundances of Prevotella, Bifidobacterium, Bacteroides, and Subdoligranulum were effective in differentiating between the UISS and NC groups. Conclusion: Alterations in intestinal microbiota may be associated with ISS. Specific bacterial species, such as Prevotella, may be potential diagnostic markers for ISS. What is Known: • ISS is associated with the GH-IGF-1 axis. • Recent studies indicated an association between the GH-IGF-1 axis and intestinal microbiota. What is New: • Children with ISS showed alterations in intestinal microbiota, with a relative increase in the abundance of gut inflammation-related bacteria. • The relative abundances of Prevotella, Bacteroides, Bifidobacterium, and Subdoligranulum may serve as potential diagnostic markers. [ABSTRACT FROM AUTHOR]