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The aim of this study was to compare different bacteriological aspects of the respiratory systems of healthy (H) versus unhealthy (UH) animals with respiratory signs. The prevalence of different bacterial species was determined in the upper and lower respiratory tract of H and UH Najdi sheep, Somali sheep and Holstein calves. The characteristics of Pasteurella spp. isolates, and the biotype of Pasteurella haemolytica were identified in H and UH animals. Eighteen out of 28 (64.3%) of the identified bacterial species in the upper respiratory tract were more prevalent in the nasal cavities of UH Najdi and Somali sheep and Holstein calves with respiratory signs than in apparently healthy animals; four of the most prevalent bacteria in the upper respiratory system of UH sheep were Moraxella spp., Pseudomonas pseudomallei, Erysipelothrix spp., and Pasteurella multocida, while three of the most prevalent bacteria in UH calves were Pasturella haemolytica, Actinomyces spp., and Pseudomonas aeruginosa. The prevalence of six different bacterial species was greater in the lungs of UH animals, namely Actinomyces pyogenes, Erysipelothrix spp., P. haemolytica, Pasteurella ureae, Staphylococcus aureus, and Staphylococcus epidermidis, which could be risk factors in the complexity of the prevalent respiratory diseases of the animals surveyed.Of the biochemical, cytological and colonial characteristics studied in the identified P. haemolytica and P. multocida, two characters were significantly different (p < 0.05) in organisms isolated from UH as compared to those from H animals. These were the higher loss of haemolytic power by the strains of P. haemolytica and the decreased fermentation of trehalose by all the strains of P. multocida recovered from healthy animals.The only biotype of P. haemolytica isolated from H animals was biotype A, while both biotypes A (88.0% of the isolates) and T (12.0% of the isolates) were recovered from UH animals.