Purpose: This study investigated microbiome and metabolome differences between ulcerated tissues and normal skin from the lower limbs of participants with leprosy. 
Patients and Methods: Ulcerated tissues and surrounding normal skin were collected from the lower limbs of 28 participants with leprosy who had been cured. The 16S ribosomal DNA sequencing analysis of the samples was conducted with the Illumina NovaSeq platform to analyze the community structure and diversity of microorganisms on the skin surface, followed by non-targeted metabolomic analysis with LC-MS technology. Next, differential metabolites were statistically screened, followed by metabolic pathway analysis. The Spearman method was used to analyze the correlation between differential microbiota and differential metabolites. 
Results: Compared to normal skin, ulcerated tissues showed a decrease in microbial α diversity (species richness, homogeneity, and sequencing depth), without significant differences (observed species, Chao1, Shannon, Simpson, and Pielou’s evenness index; P > 0.05). Conversely, Jaccard distance demonstrated that sample β-diversity exhibited a certain degree of clustering (P < 0.05), with significant differences between the two groups. The results of LEfSe analysis revealed that compared to the normal skin, the ulcerated tissues had significantly decreased microbial abundance of Flavobacteriaceae, Flavobacteriales, Lachnospiraceae, Lachnospirales, Enterobacterales, Acinetobacter, and Moraxellaceae, which might be associated with the ulcerative state. The Spearman correlation analysis suggested a strong correlation between skin metabolome and skin microbiome. 
Conclusion: For participants with leprosy sequelae, skin microecology and metabolites are disturbed and species diversity and homogeneity are reduced in lower-limb ulcers, and the types of skin metabolites are dependent on the microbiota. 
 
Keywords: leprosy, lower-limb ulcers, 16S rDNA sequencing, metabolome, skin microecology