The normal flora, or commensal microbiota, is the vast population of microorganisms residing on and within the human body. These microscopic residents include bacteria, fungi, archaea, and viruses, and they typically exist without causing disease. These microbes are not mere passengers; they exist in a symbiotic relationship with the host, where both parties benefit. An adult human harbors approximately 39 trillion bacterial cells, a number roughly equivalent to the number of human cells. The collective genetic material of these microbes is referred to as the human microbiome, and its influence on health is a major focus of modern science.
Where the Microbes Reside
The distribution of normal flora is not uniform across the body, depending instead on the unique environmental conditions of specific anatomical niches. Areas exposed to the external environment, such as the skin and mucous membranes, are heavily colonized. Conversely, internal tissues and body fluids like blood, cerebrospinal fluid, and the lower respiratory tract are typically sterile in a healthy person. The skin hosts a resident flora composed largely of Gram-positive organisms like Staphylococcus epidermidis and Propionibacterium acnes, which thrive in its varied microenvironments.
The gastrointestinal tract represents the densest microbial habitat, with concentrations increasing dramatically along its length. The stomach’s high acidity keeps its microbial population low. However, the large intestine can contain up to $10^{11}$ bacteria per gram of contents, primarily strict anaerobes like Bacteroides and Bifidobacterium species. The mouth and upper respiratory tract also maintain a diverse community, including various streptococci and Neisseria species. The local environment, including pH, oxygen levels, and available nutrients, determines which microbial species can establish a fixed community.
The Protective Roles of Normal Flora
The host derives numerous benefits from its microbial residents, primarily tied to their metabolic activities. One primary function is colonization resistance, where the resident flora physically and chemically prevents pathogenic invaders from gaining a foothold. Microbes achieve this by competing with newcomers for limited resources and physical attachment sites on host cells. They also produce inhibitory substances, such as short-chain fatty acids (SCFAs) like acetate and butyrate, which suppress the growth of external pathogens like Salmonella.
Beyond defense, the gut flora plays a significant role in nutrient processing that the human host cannot perform alone. These microbes possess enzymes capable of breaking down complex carbohydrates and dietary fiber into forms the body can absorb. They are also responsible for synthesizing certain vitamins, notably Vitamin K, which is required for blood clotting, and several B vitamins. The constant exposure to these commensals is essential for immune system training, helping the immune system mature and learn to distinguish between harmless foreign entities and true threats.
Establishing the Microbial Community
The establishment of this complex microbial community begins immediately at birth, marking the first major colonization event. The mode of delivery significantly influences the newborn’s initial microbial profile. Infants born vaginally are colonized by microbes from the mother’s vaginal and gut microbiota, including species like Lactobacillus. Conversely, infants delivered by C-section often acquire microbes resembling the mother’s skin flora, such as Staphylococcus and Corynebacterium species.
Early life diet acts as another powerful factor shaping the infant microbiome, particularly in the gut. Breastfeeding promotes the growth of beneficial bacteria, such as Bifidobacterium, which help train the immune system. As a person ages, external influences like diet, environment, geography, and antibiotic use continue to modulate the composition of the microbial community. While the core resident flora is relatively stable, it constantly adapts to these environmental pressures, reflecting the dynamic nature of this internal ecosystem.
When Commensals Turn Pathogenic
While the normal flora provides substantial benefits, its members can become agents of disease under certain circumstances. This phenomenon is known as opportunistic infection, where generally harmless microbes take advantage of a change in host conditions. If a breach occurs in the physical barrier, such as through surgery or injury, gut bacteria like Bacteroides or E. coli can enter the sterile bloodstream or abdominal cavity. This can lead to life-threatening infections like sepsis or peritonitis.
Another common pathway to disease involves a disruption of the microbial balance, termed dysbiosis. This imbalance often occurs after the use of broad-spectrum antibiotics, which kill off large numbers of beneficial bacteria along with targeted pathogens. The resulting lack of competition allows opportunistic species, such as the yeast Candida albicans or the bacterium Clostridioides difficile, to overgrow and cause infection. Dysbiosis is increasingly linked to broader health issues, demonstrating that maintaining the correct microbial balance is fundamental to overall well-being.