A peptidome-based phylogeny pipeline reveals differential peptides at the strain level within Bifidobacterium animalis subsp. lactis

•Some B. lactis strains are considered probiotics, as they exert beneficial effects on the human host.•Current strains used in food nutrition show limited genetic variability, making difficult to differentiate among strains.•Our peptidome-based analysis using whole proteomes to obtain peptidomes simulating gut endopeptidases in silico.•This pipeline allowed detecting strain-specific peptides.•Differential peptides may have applications for detecting specific strains in functional foods or in the gut microbiota.

Bifidobacteria are gut commensal microorganisms belonging to the Actinobacteria group. Some specific strains of Bifidobacterium animalis subsp. lactis are used in functional foods as they are able to exert health-promoting effects in the human host. Due to the limited genetic variability within this subspecies, it is sometimes difficult for a manufacturer to properly track its strain once included in dairy products or functional foods. In this paper, we present a peptidome-based analysis in which the proteomes of a set of B. animalis subsp. lactis strains were digested in silico with human gut endopeptidases. The molecular masses were compared along all the strains to detect strain-specific peptides. These peptides may be interesting towards the development of methodologies for strain identification in the final product.