Abstract: In this study, 14 strains of Lacticaseibacillus rhamnosus isolated from the feces of healthy infants in the Hulun Buir area of Inner Mongolia were used. By means of whole genome sequencing, comparative genomics and phenotypic metabolic capacity analysis, the association between the genomic characteristics of the strains and their carbohydrate metabolic capacity was systematically analyzed. Genomic analysis indicated that the average genome size was (2.89 ± 0.06) Mb, and the average GC content was (46.71 ± 0.06)%. Functional annotations showed that all strains exhibited significant gene enrichment in in the pathways of carbohydrate metabolism, amino acid metabolism and energy metabolism. Further analysis revealed that the three representative strains, WM-1, WM-2 and WM-5, had significantly more genes related to metabolism (Kyoto Encyclopedia of Genes and Genomes (KEGG)), carbohydrate transport and metabolism (Evolutionary Genealogy of Genes: Non-Supervised Orthologous Groups (eggNOG)), and carbohydrate active enzymes (Carbohydrate-Active enZYmes (CAZy), especially the glycoside hydrolase (GH) and glycosyltransferase (GT) families) than other strains. Specific gene enrichment analysis revealed that these strains exhibited the most significant gene enrichment in starch and sucrose metabolism, histidine metabolism, and the phosphotransferase system (PTS) pathway. The results of metabolic phenotype analysis confirmed that WM-1, WM-2 and WM-5 had stronger utilization capabilities for various carbon sources such as glucose, sucrose, trehalose, galactose and L-rhamnose. Canonical correspondence analysis (CCA) and RV coefficient permutation test (RV = 0.467 7, P = 0.011 8) indicated that there was a significantly positive correlation between the carbon source utilization spectra of the strains and their genome-encoded carbohydrate metabolic potential. In summary, this study clarified the genetic characteristics of infantile Lacticaseibacillus rhamnosus associated with core carbohydrate metabolism, and identified three strains with superior metabolic capacities, WM-1, WM-2, and WM-5. The carbohydrate metabolism capacity predicted by their genomes was highly consistent with the results of metabolokinetic analysis. The findings of this study provide an important genetic basis for future screening of these strains for use as probiotics.

Key words: Lacticaseibacillus rhamnosus; whole genome sequencing; carbohydrate metabolism; phenotype-genotype association