Background/Objectives: The growing number of households with companion dogs raises concerns. Co-living environments between companion dogs and their owners are linked to a heightened risk of cross-infections from strains such as Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), Salmonella, and faecal coliforms. Therefore, this study aims to propose measures for healthy cohabitation by analysing the faecal microbiota of puppies and adult dogs. Methods: We isolated lactic acid bacteria (LAB) from their faeces and assessed their potential to inhibit E. coli, S. aureus, and Salmonella spp. Faecal samples from puppies (12 months old) were analysed and compared. Results: The analysis revealed that Lactobacillus dominated puppy faeces, while Bacteroidetes were more abundant in adult dogs. In total, 109 primary LAB candidates were isolated from faecal samples. These isolates underwent secondary screening for acid tolerance, bile salt resistance, acid production, heat resistance, protease activity, and antimicrobial activity against E. coli, S. aureus, and Salmonella spp. Five secondary LAB candidates with probiotic potential were further characterised via morphological and genetic analysis. All five strains were Lactobacillus reuteri, with L. reuteri JJ37, JJ68, JJ69, JJ71, and JJ77 emerging as the final probiotic candidates. Conclusions: They promote healthier cohabitation between dogs and their owners.

Background/ Objectives: The growing number of households with companion dogs raises concerns. Co-living environments between companion dogs and their owners are linked to a heightened risk of cross-infections from strains such as Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), Salmonella, and faecal coliforms. Therefore, this study aims to propose measures for healthy cohabitation by analysing the faecal microbiota of puppies and adult dogs. Methods: We isolated lactic acid bacteria (LAB) from their faeces and assessed their potential to inhibit E. coli, S. aureus, and Salmonella spp. Faecal samples from puppies (< 2 months old) and adult dogs (> 12 months old) were analysed and compared. Results: The analysis revealed that Lactobacillus dominated puppy faeces, while Bacteroidetes were more abundant in adult dogs. In total, 109 primary LAB candidates were isolated from faecal samples. These isolates underwent secondary screening for acid tolerance, bile salt resistance, acid production, heat resistance, protease activity, and antimicrobial activity against E. coli, S. aureus, and Salmonella spp. Five secondary LAB candidates with probiotic potential were further characterised via morphological and genetic analysis. All five strains were Lactobacillus reuteri, with reuteri JJ37 and JJ69 emerging as the final probiotic candidates. Conclusions: It promoting healthier cohabitation between dogs and their owners.