A healthy person lives in harmony with the microbial flora that helps protect its host from invasion by pathogens, usually defined as microorganisms that have the capacity to cause disease. The microbial flora is mostly bacteria and fungi and includes normal resident flora, which is present consistently and which promptly reestablishes itself if disturbed, and transient flora, which may colonize the host for hours to weeks but does not permanently establish itself. Organisms that are normal flora can occasionally cause disease, especially when defenses are disrupted.
Tropisms (attractions to certain tissues) determine which body sites microorganisms colonize. Normal flora is influenced by tropisms and many other factors (eg, diet, hygiene, sanitary conditions, air pollution). For example, lactobacilli are common in the intestines of people with a high intake of dairy products; Haemophilus influenzae colonizes the tracheobronchial tree in patients with COPD (chronic obstructive pulmonary disease). As a result, different body habitats contain microbial communities, forming microbiomes that differ by microbial composition and function.