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We collected 24 vaginal samples and 16 fecal samples from 10 girls aged 3\u20139 years with vulvovaginitis and 16 healthy girls of the same age. The samples were divided into three groups: fecal swabs from healthy controls (HF), vaginal swabs from healthy controls (HVS), and vaginal swabs from girls with vulvovaginitis (VVS). Sequencing of the V3\u2013V4 region of the 16S rDNA gene was performed with the NovaSeq PE250 platform to reveal the vaginal microbial community structure in healthy prepubertal girls and vulvovaginitis-associated microbiota. The intestinal microbiomes of healthy children were also analyzed for comparison. This study revealed that the healthy vaginal tract in prepubertal girls was dominated by <jats:italic>Prevotella<\/jats:italic>, <jats:italic>Porphyromonas<\/jats:italic>, <jats:italic>Ezakiella<\/jats:italic>, and <jats:italic>Peptoniphilus<\/jats:italic> species, with a high diversity of microbiota. The vulvovaginitis-associated microbiota were dominated by <jats:italic>Streptococcus<\/jats:italic>, <jats:italic>Prevotella<\/jats:italic>, <jats:italic>Haemophilus<\/jats:italic>, and <jats:italic>Granulicatella<\/jats:italic>, with lower diversity than that in healthy girls. Furthermore, the compositions of the vaginal and intestinal microbiomes were completely different. ANOSIM, MRPP, Adonis, and AMOVA were used to analyze the beta diversity, and the results showed that there were significant differences in the microbial communities among the three groups. <jats:italic>Lactobacillus<\/jats:italic> deficiency and high bacterial diversity were characteristics of the vaginal microbiome in healthy prepubertal girls; this is inconsistent with that in reproductive-age women. The vulvovaginitis-associated vaginal microbiota differed dramatically from normal microbiota, and the main causative agents were not fecal in origin.<\/jats:p>","DOI":"10.1007\/s10096-021-04152-2","type":"journal-article","created":{"date-parts":[[2021,1,16]],"date-time":"2021-01-16T09:03:48Z","timestamp":1610787828000},"page":"1253-1261","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["Characteristics of the vaginal microbiomes in prepubertal girls with and without vulvovaginitis"],"prefix":"10.1007","volume":"40","author":[{"given":"Wu","family":"Xiaoming","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liu","family":"Jing","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pan","family":"Yuchen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liu","family":"Huili","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhang","family":"Miao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shu","family":"Jing","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,1,16]]},"reference":[{"key":"4152_CR1","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1136\/adc.2009.181883","volume":"96","author":"AS Garden","year":"2011","unstructured":"Garden AS (2011) Vulvovaginitis and other common childhood gynecological conditions. 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