Why do organisms in the upper respiratory tract [might] change when the normal flora is replaced with transient flora
Normal flora lives within the nose, pharynx and trachea of the human respiratory system. Nearly all of the surfaces of the respiratory tract (nasal and oral passages, nasopharynx, oropharynx, trachea, bronchi, bronchioles, and alveolar sacs) are colonized by the host microbiota. These organisms are inhabitants of the respiratory tract and rarely, if ever, cause disease. The microbiota of the respiratory tract has two main functions important in maintaining the healthy state of the host because these organisms compete with pathogenic organisms for potential attachment sites, and they can produce substances that are bactericidal and prevent infection by pathogens.
Transient flora is flora that is introduced to the body and can cause infection. To protect themselves from the alveolar macrophages most pathogenic bacteria produce a capsule that inhibits phagocytosis. Other pathogenic microorganisms escape alveolar macrophage killing by reproducing/surviving in the cells that line the respiratory tree (e.g., Influenza virus) or by reproducing/surviving in the alveolar macrophages.