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.

Gram staining is a laboratory technique that helps to classify bacteria into two major groups: gram-positive and gram-negative, based on the physical and chemical properties of their cell walls. The technique was developed by a Danish physician, Hans Christian Gram, in 1884.

Gram staining involves four steps: applying a primary stain (crystal violet) to a heat-fixed smear of bacterial culture, followed by a mordant (iodine), rapid decolorization with alcohol or acetone, and a counterstain (safranin). After staining, the smear is examined under a microscope.

The cell walls of gram-positive bacteria have a thick layer of peptidoglycan, which retains the crystal violet dye during decolorization. Therefore, gram-positive bacteria appear purple under the microscope. The cell walls of gram-negative bacteria have a thin layer of peptidoglycan and an outer membrane of lipopolysaccharide, which loses the crystal violet dye during decolorization and takes up the safranin dye. Therefore, gram-negative bacteria appear pink or red under the microscope.

Gram staining is an important tool for identifying and characterizing bacteria based on their gram reaction. It also helps to choose appropriate antibiotics for treating bacterial infections, as gram-positive and gram-negative bacteria differ in their susceptibility to various antimicrobial agents.

Some examples of gram-positive and gram-negative bacteria that are normal flora of the mouth and gastrointestinal tract are:

• Gram-positive bacteria: Staphylococcus spp., Streptococcus spp., Clostridium spp., Bacillus spp., Corynebacterium spp., Actinomyces spp., Lactobacillus spp., Enterococcus spp.
• Gram-negative bacteria: Helicobacter pylori, Fusobacterium spp., Propionibacterium spp., Campylobacter spp., Rothia spp., Actinobacillus spp., Eubacterium spp., Gemella spp., Peptostreptococcus spp., E. coli, Klebsiella spp., Enterobacter spp., Citrobacter spp., Vibrio spp., Proteus spp., Leminorella spp., Providencia spp., Yersinia spp., Bacteroides spp.

The mouth and the gastrointestinal tract are home to a diverse and complex community of microorganisms, collectively known as the normal flora or microbiota. These microorganisms colonize different parts of the mouth and the gastrointestinal tract, depending on their physiological and metabolic characteristics, as well as the environmental conditions and host factors.

The mouth is the first part of the gastrointestinal tract and contains several distinct habitats for microorganisms, such as the teeth, the tongue, the gingival crevices, the hard and soft palates, the cheeks, and the tonsils. The oral microbiota consists of more than 700 different species of bacteria, as well as fungi, protozoa, and viruses. The most abundant bacterial groups in the mouth are Streptococcus, Actinomyces, Veillonella, Fusobacterium, Prevotella, Porphyromonas, Neisseria, Haemophilus, and Rothia. Some of these bacteria are involved in dental plaque formation and dental caries development, while others play a protective role against pathogens or modulate the host immune response.

The gastrointestinal tract is a long tube that extends from the mouth to the anus and consists of several segments with different functions: the esophagus, the stomach, the small intestine (duodenum, jejunum, and ileum), and the large intestine (cecum, colon, rectum, and anus). The gastrointestinal microbiota is composed of more than 1000 different species of bacteria, as well as archaea, fungi, protozoa, and viruses. The bacterial diversity and density increase along the gastrointestinal tract, reaching the highest levels in the colon. The most dominant bacterial phyla in the gastrointestinal tract are Firmicutes (e.g., Clostridium, Lactobacillus), Bacteroidetes (e.g., Bacteroides), Actinobacteria (e.g., Bifidobacterium), Proteobacteria (e.g., Escherichia), and Verrucomicrobia (e.g., Akkermansia). Some of these bacteria are beneficial for the host by producing vitamins, fermenting dietary fibers, regulating metabolism, modulating immunity, and preventing colonization by pathogens. However, some bacteria can also cause infections or inflammation under certain conditions.

The following table summarizes some of the specific locations of normal flora in mouth and gastrointestinal tract:

Gram-positive bacteria are bacteria that have a thick cell wall composed of peptidoglycan and stain purple when subjected to the Gram stain technique. They are one of the major groups of bacteria that inhabit the human mouth and gastrointestinal tract. Some of the common genera of gram-positive bacteria in the mouth and gastrointestinal tract are:

• Staphylococcus: These are spherical (cocci) bacteria that form grape-like clusters and are catalase-positive, coagulase-positive or negative, and aerobic. They are transient flora of the mouth and oropharynx, especially in children. The most dominant species in the mouth and oropharynx are S. epidermidis and S. aureus.
• Streptococcus: These are spherical (cocci) bacteria that form chains and are catalase-negative, anaerobic or facultative anaerobic. They are present in every part of the GI tract and are mostly considered transient flora. Some of the common species in the GI tract are S. agalactiae, S. mutans, S. mitis, S. oralis, S. parasanguis, S. sanguis, S. salivarius, S. cristatus, S. constellatus, S. anginosus group, etc.
• Clostridium: These are rod-shaped (bacilli) bacteria that are strictly anaerobic and spore-forming. They are the predominant commensal bacteria in the gut, covering about 10 – 40% of total gut bacteria. Some of the common species in the human intestine are C. aerotolerans, C. aminophilus, C. aminovalericum, C. clostridiiforme, C. coccoides, C. nexile, C. oroticum, C. polysaccharolyticum, C. symbiosum, C. leptum, C. difficile strain 630, C. sordelli, C. absonum, C. butyricum, C. paraputrificum, C. xylanolyticum, etc.
• Bacillus: These are rod-shaped (bacilli) bacteria that are motile, obligate aerobic or some facultative anaerobic, and spore-forming. Some of the common species in the human intestine are B. clausii, B. licheniformis, B. coagulans.
• Corynebacterium: These are rod-shaped (bacilli) bacteria that are club-shaped, aerobic, and have high mesodiaminopimelic acid and highly repeated arabinogalactan in their cell wall. One of the common species in the oral cavity is C. matruchotii. Corynebacterium species are also found in the large intestine.
• Actinomyces: These are rod-shaped (bacilli) bacteria that are branched, obligate anaerobic or facultatively anaerobic, and endospore-forming. Some of the common species in the mouth are A. viscous, A. naeslundii, A. israelii. Some species are also found in the small and large intestine as transient flora.
• Lactobacillus: These are rod-shaped (bacilli) bacteria that are non-motile, non-sporing, anaerobic or microaerophilic, and lactic acid fermenting (LAB). They are normal flora of the mouth, GI tract, and the female reproductive tract. More than 50 species of Lactobacillus are found in the intestine of healthy humans. Some of the most abundant species are L. casei, L. delbruckeii, L. murinus, L. plantarum, L. rhamnosus, and L. ruminus.
• Enterococcus: These are spherical (cocci) bacteria that form pairs or chains and are facultatively anaerobic, lactose fermenting, and bile salt tolerant up to 40%. Enterococci are commensals of the GI tract and some of the common species are E. faecalis and E. faecium.

These gram-positive bacteria play important roles in maintaining oral health, digestion, immunity, and metabolism. However, some of them can also cause infections and diseases if they overgrow or invade other parts of the body. Therefore, it is essential to maintain a balanced and diverse microbiota in the mouth and gastrointestinal tract.

Gram-negative bacteria are bacteria that have a thin layer of peptidoglycan in their cell wall and stain red with the Gram stain. They also have an outer membrane that contains lipopolysaccharides (LPS), which are endotoxins that can trigger inflammation and septic shock. Gram-negative bacteria are often more resistant to antibiotics than gram-positive bacteria because of their outer membrane and efflux pumps that can expel drugs.

Gram-negative bacteria are present in various locations of the mouth and gastrointestinal tract, where they can be part of the normal flora or cause infections. Some of the common gram-negative bacteria in the mouth and gastrointestinal tract are:

• Helicobacter pylori: This is a helical, microaerophilic bacterium that colonizes the stomach and duodenum of about 50% of humans. It can cause gastritis, peptic ulcers, gastric cancer, and mucosa-associated lymphoid tissue (MALT) lymphoma. It is transmitted through oral-oral or fecal-oral routes and can survive the acidic environment of the stomach by producing urease, which neutralizes the acid.
• Fusobacterium spp.: These are anaerobic, rod-shaped bacteria with pointed ends that are found in the mouth and intestine. They can cause abscesses, wound infections, and pulmonary and intracranial infections. They are often involved in mixed infections with other anaerobes or facultative anaerobes. They can adhere to epithelial cells and produce toxins that damage tissues.
• Porphyromonas spp.: These are anaerobic, rod-shaped bacteria that are part of the normal flora of the oral cavity. They can cause periodontitis, aspiration pneumonia, and brain abscesses. They can degrade collagen and other host proteins and produce volatile sulfur compounds that cause halitosis (bad breath).
• Prevotella spp.: These are anaerobic, rod-shaped bacteria that are found in the oral cavity and intestine. They can cause intra-abdominal and soft-tissue infections. They can ferment carbohydrates and produce short-chain fatty acids that lower the pH of the environment.
• Campylobacter spp.: These are comma-shaped, motile, microaerophilic bacteria that are found in the intestine and mouth. They can cause gastroenteritis, enterocolitis, bacteremia, and Guillain-Barré syndrome. They are transmitted through contaminated food, water, or animals and can invade the intestinal mucosa and produce toxins that damage the epithelial cells.
• Escherichia coli: This is a rod-shaped, motile, lactose-fermenting, facultative anaerobic bacterium that is one of the most common aerobic microflora species of the human intestines. It can cause urinary tract infections, diarrhea, sepsis, meningitis, and hemolytic uremic syndrome. It is transmitted through fecal-oral route or contact with animals and can produce various virulence factors such as adhesins, toxins, capsules, flagella, pili, and siderophores.
• Klebsiella spp.: These are rod-shaped, non-motile, encapsulated, lactose-fermenting, facultative anaerobic bacteria that are part of the Enterobacteriaceae family. They are found in the intestine and can cause pneumonia, urinary tract infections, septicemia, wound infections, and liver abscesses. They are transmitted through contact with contaminated surfaces or medical devices and can produce capsules that protect them from phagocytosis and antibiotics.
• Enterobacter spp.: These are rod-shaped, motile, lactose-fermenting, facultative anaerobic bacteria that are part of the Enterobacteriaceae family. They are found in the small and large intestine and can cause urinary tract infections, wound infections, septicemia, meningitis, and respiratory tract infections. They are transmitted through contact with contaminated surfaces or medical devices and can produce biofilms that enhance their survival and resistance.
• Citrobacter spp.: These are rod-shaped, lactose-fermenting bacteria that are part of the Enterobacteriaceae family. They are found in the intestine and can cause urinary tract infections, wound infections, septicemia, and respiratory tract infections. They are transmitted through contact with contaminated surfaces or medical devices.

The mouth and gastrointestinal tract of humans are home to a diverse and complex community of microorganisms, collectively known as the normal flora or microbiota. These microorganisms play important roles in maintaining the health and function of the host, such as aiding in digestion, producing vitamins, preventing colonization by pathogens, and modulating the immune system. The normal flora of the mouth and gastrointestinal tract can be classified by their Gram staining characteristics, which reflect their cell wall structure and composition. Gram-positive bacteria have a thick layer of peptidoglycan in their cell wall, while Gram-negative bacteria have a thin layer of peptidoglycan and an outer membrane containing lipopolysaccharide. The normal flora of the mouth and gastrointestinal tract can also be identified by their specific locations, which depend on factors such as pH, oxygen availability, nutrient availability, and host factors. The normal flora of the mouth and gastrointestinal tract consists of both aerobic and anaerobic bacteria, with anaerobes being more predominant in the lower parts of the gastrointestinal tract. The normal flora of the mouth and gastrointestinal tract includes bacteria from various genera and families, such as Staphylococcus, Streptococcus, Clostridium, Bacillus, Corynebacterium, Actinomyces, Lactobacillus, Enterococcus, Helicobacter, Fusobacterium, Propionibacterium, Campylobacter, Rothia, Actinobacillus, Eubacterium, Gemella, Peptostreptococcus, Escherichia coli, Klebsiella, Enterobacter, Citrobacter, Vibrio, Proteus, Leminorella, Providencia, Yersinia, and Bacteroides. Each of these bacteria has its own characteristics and functions that contribute to the overall balance and harmony of the normal flora of the mouth and gastrointestinal tract. However, some of these bacteria can also cause diseases or infections if they overgrow or invade other parts of the body. Therefore, it is important to maintain a healthy and stable normal flora of the mouth and gastrointestinal tract by following good oral hygiene practices and eating a balanced diet that supports the growth of beneficial bacteria. By doing so, we can enjoy the benefits of having a diverse and complex normal flora of the mouth and gastrointestinal tract that helps us stay healthy and happy. 😊

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