Genomic Characterization of the Probiotic Limosilactobacillus mucosae CRL2069 Isolated from Feedlot Cattle Feces

Limosilactobacillus mucosae (L.) CRL2069, isolated from feedlot cattle feces, has previously exhibited high performance when used as a probiotic in animals. To investigate the genetic bases underlying its probiotic potential, complete genome sequencing and comparative analyses were performed. The CRL2069 genome showed a total length of 1.93 Mb, with an average GC content of 46.76%. No evidence of plasmid sequences was detected, while CRISPR-Cas elements, as well as twelve genomic islands, were identified in the genome. Pan-genomic and clustering analysis among L. mucosae strains showed a lack of partitioning according to their isolation origin, revealing a niche specialization. CRL2069 genes related to stress and those conferring probiotic character were identified. In addition, the absence of acquired antimicrobial resistance genes and virulence determinants evidenced the safety of this strain. Genomic determinants conferring the ability to metabolize a diverse array of carbohydrates, particularly those present in cattle feed, were annotated. Phenotypic analysis supported the genomic prediction and demonstrated the capacity of CRL2069 to metabolize 39 out of 95 carbon sources tested and to produce folate. Based on the results obtained, L. mucosae CRL2069 evaluated in this study is confirmed to be a promising candidate for use as a probiotic in cattle.