The human body is a dynamic ecosystem inhabited by trillions of microorganisms, including bacteria, fungi, and viruses, collectively known as the human microbiota. Many of these microbes exist in a commensal relationship with the body, meaning they benefit from the environment without affecting the host. This community, often referred to as commensal flora, populates nearly every surface of the body exposed to the external world.
Where Commensal Flora is Found
The most densely populated microbial habitat in the human body is the gastrointestinal tract, particularly the large intestine. The colon alone is estimated to harbor about 38 trillion bacteria. The gut microbiota is dominated by two major bacterial phyla, Bacteroidetes and Firmicutes. These organisms thrive in the anaerobic environment of the large intestine, where they find a rich supply of nutrients from undigested food.
The skin is also a large and varied habitat for commensal flora, with distinct microbial communities adapted to different environments. These areas can be broadly categorized as oily, moist, and dry. Oily or sebaceous sites like the face and back are often dominated by lipophilic bacteria, such as Cutibacterium acnes. Moist areas, including the armpits and elbow creases, support populations of Corynebacterium and Staphylococcus. Staphylococcus epidermidis is a particularly widespread skin commensal, found across all skin types but showing a preference for moist environments.
Another significant site of microbial colonization is the oral cavity. The mouth provides a unique environment with hard and soft surfaces, supporting a diverse array of bacteria. Streptococcus species, such as Streptococcus mutans, are common inhabitants that adhere to tooth surfaces, forming part of the biofilm known as dental plaque. Smaller microbial populations also reside in the respiratory and urogenital tracts. The vaginal microbiome, for example, is characterized by a low-diversity community dominated by Lactobacillus species.
The Function of Commensal Flora
One of the most well-understood roles of the microbiota occurs in the gut, where microbes are instrumental in nutrient metabolism. Human cells lack the enzymes needed to break down complex carbohydrates like dietary fiber. Gut bacteria ferment these indigestible fibers, producing beneficial byproducts called short-chain fatty acids (SCFAs), such as butyrate, propionate, and acetate. Butyrate serves as a primary energy source for the cells lining the colon, while all SCFAs contribute to overall metabolic regulation.
The development of a healthy immune system is closely linked to the microbiota. Exposure to commensal microbes, beginning at birth, helps the immune system mature. These interactions train immune cells to distinguish between harmless resident microbes and invading pathogens. This training process helps establish a balanced immune response, preventing reactions that could lead to inflammation or autoimmune conditions. For example, specific bacteria can influence the development of T-cells, which coordinate the body’s defense mechanisms.
These microbial communities also offer protection against pathogens through a mechanism known as competitive exclusion. By occupying physical niches on mucosal surfaces and consuming available nutrients, commensal microbes make it difficult for harmful bacteria to gain a foothold. Some resident bacteria can also produce antimicrobial substances that directly inhibit the growth of competing pathogens. This competition helps maintain a stable microbial balance, forming a living barrier against infection.
Acquisition of the Microbiome
An individual’s microbiome is not innate; it is acquired and assembled starting at birth. The mode of delivery is a significant factor in the initial colonization process. During a vaginal birth, an infant is exposed to the mother’s vaginal and fecal microbiota, seeding the gut with bacteria like Bifidobacterium and Bacteroides. In contrast, infants born via Cesarean section are first exposed to microbes from the skin and the hospital environment, resulting in a different initial microbial profile.
Following birth, feeding methods become a primary influence on the developing gut microbiota. Breast milk is a rich source of not only nutrition but also microbes and compounds that foster the growth of beneficial bacteria. The gut microbiomes of breastfed infants tend to be dominated by Bifidobacterium and Lactobacillus species. Formula-fed infants often show a more diverse community of bacteria that differs in composition from that of breastfed babies.
The microbiome continues to evolve throughout infancy and early childhood, shaped by a wide range of environmental factors. Diet plays a role as solid foods are introduced, supporting different bacterial populations. Close contact with family members, caregivers, and even pets introduces new microbes. The broader environment, including the home and outdoors, also contributes to the unique microbial signature that each person develops.
Disruption of the Microbial Balance
The stable coexistence between the host and its microbiota can be disturbed, leading to an imbalance known as “dysbiosis.” This condition is characterized by a change in the microbial community, such as a loss of beneficial organisms, an overgrowth of potentially harmful ones, or a reduction in diversity. Dysbiosis disrupts the normal functions of the microbiota and is associated with various health issues.
One of the most common causes of dysbiosis is the use of antibiotics. While effective at targeting pathogenic bacteria, broad-spectrum antibiotics are not selective and can also eliminate large populations of beneficial commensal microbes. This collateral damage can create an opportunity for less desirable or antibiotic-resistant organisms to proliferate.
Diet also has a substantial impact on microbial balance. A diet low in fiber or high in processed foods and sugar can alter the gut environment. This change favors the growth of some bacteria over others and leads to an imbalanced community.
When the microbial balance is upset, some normally harmless commensal microbes can become opportunistic pathogens. These organisms do not cause disease under normal circumstances but can take advantage of a disruption to cause an infection. A classic example is Escherichia coli, a standard inhabitant of the human gut that can cause a urinary tract infection (UTI) if introduced into the urinary tract. Similarly, the fungus Candida albicans, a common member of the oral and urogenital flora, can overgrow after a course of antibiotics, leading to oral thrush or a yeast infection.