Normal Flora (Microbiota) of Mouth and Gastrointestinal Tract


The human body is home to a diverse and complex community of microorganisms, collectively known as the normal flora or microbiota. These microorganisms include bacteria, fungi, viruses and protozoa that live in harmony with the host under normal conditions, and provide various benefits such as digestion, immunity, metabolism and protection from pathogens. The normal flora varies in composition and abundance depending on the anatomical site, age, diet, health status and environmental factors of the host.

One of the most densely populated and diverse sites of the human body is the mouth and gastrointestinal tract (GI tract), which extends from the oral cavity to the anus. The mouth and GI tract are exposed to a variety of external influences, such as food, water, saliva, mucus, bile and drugs, that affect the physicochemical properties and microbial ecology of each segment. The mouth and GI tract also have different anatomical structures, such as teeth, tongue, tonsils, esophagus, stomach, small intestine and large intestine, that create distinct microenvironments for microbial colonization.

The normal flora of the mouth and GI tract consists of more than 400 species of bacteria, as well as fungi (mainly Candida spp.), viruses (mainly bacteriophages) and protozoa (mainly Entamoeba spp.). The bacterial flora can be classified by Gram staining into Gram-positive and Gram-negative bacteria. Gram-positive bacteria have a thick peptidoglycan layer in their cell wall that retains the crystal violet dye during Gram staining, while Gram-negative bacteria have a thin peptidoglycan layer surrounded by an outer membrane that does not retain the dye. Gram-positive bacteria are generally more resistant to acidic and dry conditions than Gram-negative bacteria, and are more prevalent in the mouth than in the GI tract. Gram-negative bacteria are more diverse and adaptable to different environments than Gram-positive bacteria, and are more prevalent in the GI tract than in the mouth.

The normal flora of the mouth and GI tract plays important roles in human health and disease. Some of the beneficial functions of the normal flora are:

  • Digestion: The normal flora helps break down complex carbohydrates, proteins and fats that are not digested by human enzymes, producing short-chain fatty acids, vitamins (such as vitamin K and B12) and amino acids that can be absorbed by the host.
  • Immunity: The normal flora stimulates the development and maturation of the immune system, especially the mucosal immunity that protects the epithelial surfaces from pathogens. The normal flora also competes with potential pathogens for nutrients and attachment sites, produces antimicrobial substances (such as bacteriocins and hydrogen peroxide) and modulates inflammatory responses.
  • Metabolism: The normal flora influences the metabolism of drugs, hormones and toxins by modifying their bioavailability, activity and excretion. The normal flora also affects energy balance by regulating appetite, satiety and energy expenditure.
  • Protection: The normal flora prevents colonization by pathogens by forming a physical barrier on the mucosal surfaces, producing acidic pH (in the mouth and vagina) or alkaline pH (in the colon) that inhibits pathogen growth, inducing mucin secretion that traps pathogens and facilitating their clearance by peristalsis.

However, the normal flora can also cause harm to the host under certain circumstances, such as:

  • Dysbiosis: Dysbiosis is an imbalance or disruption of the normal flora due to factors such as antibiotic use, stress, diet change or infection. Dysbiosis can result in reduced diversity and functionality of the normal flora, increased susceptibility to pathogens or opportunistic infections (such as Clostridium difficile colitis or oral candidiasis), altered immune responses or metabolic disorders (such as obesity or diabetes).
  • Translocation: Translocation is the movement of bacteria from their normal site to a sterile site within or outside the body. Translocation can occur due to trauma, surgery, inflammation or ischemia that compromise the integrity of the mucosal barrier. Translocation can cause systemic infections (such as bacteremia or sepsis), local infections (such as peritonitis or abscesses) or chronic inflammation (such as inflammatory bowel disease or rheumatoid arthritis).
  • Carcinogenesis: Carcinogenesis is the process of transforming normal cells into cancerous cells. Some bacteria can contribute to carcinogenesis by producing toxins (such as Helicobacter pylori cytotoxin), inducing chronic inflammation (such as Fusobacterium nucleatum in colorectal cancer) or altering DNA methylation (such as Streptococcus gallolyticus in colon cancer).

In summary, the normal flora of the mouth and GI tract is a complex and dynamic community of microorganisms that interacts with the host and the environment, and influences various aspects of human health and disease. The normal flora can be classified by Gram staining into Gram-positive and Gram-negative bacteria, each with different characteristics and functions. The normal flora can be beneficial or harmful to the host depending on the balance, location and activity of the microorganisms. Therefore, understanding and maintaining the normal flora of the mouth and GI tract is essential for human well-being.