Objective To investigate the differences in oral and gut microbiota composition among children aged 3-5 years with varying body mass index (BMI) levels in Urumqi, and to provide a scientific basis for early microbiological warning and intervention strategies for childhood obesity.

Methods A total of 40 children aged 3-5 years were enrolled. Based on their BMI percentiles, the participants were divided into 4 groups, including the underweight, normal weight, overweight, and obesity groups (n = 10 per group). A total of 80 saliva and fecal samples were collected. Microbial community structures were analyzed using 16S rRNA gene sequencing, followed by bioinformatics and statistical analyses.

Results Oral microbiota richness, as measured by Chao1 and observed-species indices, differed significantly among the four groups (P = 0.0047 and P = 0.0054, respectively), whereas no significant difference in gut microbiota diversity was observed (P > 0.05). Beta diversity analysis revealed a distinct separation in oral microbiota between the normal-weight weight and other groups. At the genus level, obese children exhibited increased abundance in oral Leptotrichia, underweight children showed enrichment of gut Bacteroides, and overweight children showed increased abundance in gut Faecalibacterium and Blautia. Linear discriminant analysis effect size (LEfSe) analysis identified multiple biomarkers, including Prevotellaceae in the oral microbiota of normal-weight children, Catonella in the oral microbiota of obese children, and Clostridiales, Lachnospiraceae, and Hungatella in the gut microbiota of underweight children. Metabolic pathways related to lipopolysaccharide synthesis and amino acid metabolism were significantly upregulated in the microbiota of overweight and obese children.

Conclusion Significant differences are observed in the oral and gut microbiota composition among children aged 3-5 years of different BMI levels in Urumqi. Oral microbiota show greater sensitivity to BMI changes. Specific genera, such as Catonella, Leptotrichia, and Prevotellaceae, may be involved in the development of obesity. The microbiota metabolic pathways in children with high BMI are characterized by the core features of inflammation activation and lipid metabolism dysregulation.