Normal Microbiota of the Human Body

Quantitative Overview of the Human Microbiome

• The human body is a complex ecosystem heavily populated by microorganisms. In a "reference man" weighing $70\,\text{kg}$, the total number of bacteria is estimated at $3.8 \times 10^{13}$, compared to a total of $3.0 \times 10^{13}$ human cells.

• This data is sourced from PlOS Biol. 2016 Aug; 14(8): e1002533.

• Internal vs. Surface Tissues:
    - In a healthy human, internal tissues such as the brain, blood, cerebrospinal fluid, and muscles are normally free of microorganisms.
    - Surface tissues, including the skin and mucous membranes, are in constant contact with the environment and are readily colonized by specific microbial species.

Definitions and Symbiotic Relationships

• Normal Microbiota: The mixture of microorganisms regularly found at any specific anatomical site. Synonyms include indigenous microbial population, microflora, or normal flora.

• Taxonomic Composition: Bacteria constitute the majority of the normal microbiota. Fungi (primarily yeasts) and protozoa are also present but are emphasized less than bacteria.

• Modes of Association:
    - Ectosymbiosis: The organism remains outside the host.
    - Endosymbiosis: The organism is present within the host.

• Types of Relationships:
    - Mutualism: Both the host and the microbe benefit. For example, Escherichia coli in the gastrointestinal tract provides Vitamin B and Vitamin K to the host, while receiving a warm, nutrient-rich environment in return.
    - Commensalism: One organism benefits while the other remains unharmed. This describes most of the normal microbiota.
    - Parasitism/Pathogenicity: One organism (the parasite/pathogen) benefits at the expense of the host.
    - Opportunism: Microorganisms that are usually harmless but cause infection if they enter the wrong anatomical site or if the host's defenses are compromised. For example, E. coli is harmless in the digestive tract but causes infection in the urinary tract. Staphylococcus aureus in the upper respiratory tract is harmless unless growth becomes uncontrolled or it enters a wound.

Normal Microbiota of the Skin

• Surface Area and Population: The adult human skin covers approximately $2\,\text{m}^2$ and supports an estimated $10^{12}$ bacteria.

• Resident vs. Transient Microbiota:
    - Resident (Normal) Microbiota: Organisms that normally grow on or in the skin with a fixed, well-defined distribution pattern.
    - Transient Microbiota: Microorganisms temporarily present that are unable to multiply and usually die off quickly because they cannot become firmly entrenched.

• Environmental Challenges for Skin Colonization:
    - Lack of moisture: Drives many microbes into a dormant state, except in moist areas like the scalp, ears, axillary areas, genitourinary/anal regions, perineum, and palms.
    - Acidic pH: The skin maintains a pH of $4$ to $6$ due to organic acids from staphylococci and secretions from oil and sweat glands, discouraging many colonizers.
    - High Salinity: Sweat contains high concentrations of Sodium Chloride ($NaCl$), creating a hyperosmotic environment that stresses most microbes.
    - Inhibitory Substances: Sweat glands release lysozyme (muramidase), which lyses Staphylococcus epidermidis and other gram-positive bacteria by hydrolyzing the $(1 \rightarrow 4)$ glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine in peptidoglycan.

• Microbiota Interactions and Acne:
    - Oil glands (sebaceous glands) secrete complex lipids. Propionibacterium acnes degrades these into unsaturated fatty acids (e.g., oleic acid), which inhibit gram-negative bacteria and some fungi.
    - Acne vulgaris: Occurs when hormonal activity (especially during adolescence) stimulates sebum overproduction. A large volume of sebum provides a microenvironment for P. acnes. This leads to an inflammatory response, forming a comedo (a plug of sebum and keratin). This can result in papules, pustules, or nodules ("pimples" or "blackheads"). P. acnes is extremely sensitive to tetracycline.

• Common Skin Residents:
    - Coagulase-negative staphylococci (especially S. epidermidis).
    - Diphtheroids (including Propionibacterium acnes).
    - Staphylococcus aureus (primarily in nostrils and perianal regions).
    - Streptococci (various species), Bacillus spp., Malassezia furfur, and Candida spp.
    - Mycobacterium spp. (occasionally).
    - Yeasts: Pityrosporum ovale and P. orbiculare (on the scalp).
    - Clostridium perfringens: Found on the perineum and thighs, especially in diabetic patients.

Normal Microbiota of the Eye and External Ear

• External Ear: Predominantly inhabited by coagulase-negative staphylococci and Corynebacterium. Less common are Bacillus, Micrococcus, Neisseria, and gram-negative rods like Proteus, Escherichia, and Pseudomonas. Fungi include Aspergillus, Alternaria, Penicillium, Candida, and Saccharomyces.

• Conjunctiva of the Eye: Generally characterized by low numbers of commensals. Predominant species include S. epidermidis, S. aureus, aerobic corynebacteria (diphtheroids), and Streptococcus pneumoniae. Others include Branhamella catarrhalis and species of Escherichia, Klebsiella, Proteus, Enterobacter, Neisseria, and Bacillus. Anaerobes are rare.

Normal Microbiota of the Respiratory Tract

• Nose and Nasopharynx:
    - Found just inside the nostrils. Predominant species are S. aureus and S. epidermidis.
    - The nasopharynx may contain potentially pathogenic bacteria in small numbers: Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae.
    - Diphtheroids (nonpathogenic gram-positive bacteria resembling Corynebacterium) are common.

• Oropharynx:
    - Located between the soft palate and epiglottis. High populations of S. aureus and S. epidermidis.
    - Alpha-hemolytic streptococci are crucial: S. oralis, S. milleri, S. gordonii, and S. salivarius.
    - Tonsillar crypts house Micrococcus and anaerobes such as Porphyromonas, Prevotella, and Fusobacterium.

• Lower Respiratory Tract: The trachea, bronchi, bronchioles, and alveoli do not have a normal microbiota. Microbes are removed by mucus generated by ciliated epithelial cells, alveolar macrophages (phagocytosis), and lysozyme in nasal mucus.

Normal Microbiota of the Oral Cavity

• Environment: The mouth provides water, nutrients, and suitable pH and temperature for colonization. Microbes must adhere to gums or teeth to resist mechanical flushing toward the stomach.

• Successional Colonization:
    - Birth: Colonization occurs within hours, initially by Streptococcus, Neisseria, Actinomyces, Veillonella, and Lactobacillus.
    - Tooth Eruption: Anaerobe dominance increases (Porphyromonas, Prevotella, Fusobacterium) due to low-oxygen spaces between gums and teeth.
    - Tooth Surfaces: Streptococcus parasanguis and S. mutans attach to enamel using glycocalyx/adherence factors. S. salivarius attaches to buccal and gingival epithelial surfaces.
    - Contributions: These bacteria lead to dental plaque, caries, gingivitis, and periodontal disease.

Normal Microbiota of the Gastrointestinal Tract

• Stomach:
    - Highly acidic ($2$ to $3$ pH) environment kills most microbes. Volume is usually less than $10$ viable bacteria per milliliter.
    - Residents include Sarcina, Streptococcus, Staphylococcus, Lactobacillus, Peptostreptococcus, and Candida yeasts.
    - Resistance: Mycobacteria may survive due to pH resistance; others pass through via food buffering.

• Small Intestine:
    - Duodenum: First $25\,\text{cm}$. Contains few microbes due to stomach acid, bile, and pancreatic secretions. Mostly gram-positive cocci and rods.
    - Jejunum: Occasionally Enterococcus faecalis, lactobacilli, diphtheroids, and Candida albicans.
    - Ileum: Transition zone where pH becomes more alkaline. Established populations of anaerobic gram-negative bacteria and Enterobacteriaceae.

• Large Intestine (Colon):
    - Represents the largest microbial community in the body. Counts reach $10^{12}$ organisms per gram wet weight of feces. Over $400$ species identified.
    - Atmosphere: Primarily anaerobic fermentation vessel. Ratio of anaerobic to facultative anaerobic bacteria is $300:1$.
    - E. coli represents only $0.1\,\%$ of the total population.
    - Residents: Bacteroides spp. (abundant), Fusobacterium, Clostridium, Peptostreptococcus, Klebsiella, Proteus, Enterococci, Pseudomonas, Acinetobacter, and Actinomyces.
    - Protozoa: Harmless commensals like Trichomonas hominis, Entamoeba hartmanni, Endolimax nana, and Iodamoeba butschlii.
    - Factors Affecting Microbiota: Diet is a primary driver. Others include stress, altitude, starvation, antibiotics, and probiotics.

• Infant Colon Development:
    - Breast-fed: Dominated by Bifidobacterium species, facilitated by a specific disaccharide amino sugar in human milk.
    - Formula-fed: Dominated by Lactobacillus due to the absence of the specific milk factor.
    - Transition: Introduction of solid food shifts colonization toward a typical adult gram-negative microbiota.

Normal Microbiota of the Genitourinary Tract

• Sterile Sites: Kidneys, ureters, and urinary bladder are usually free of microbes.

• Urethra: Distal portion contains few bacteria: S. epidermidis, E. faecalis, Corynebacterium spp., Neisseria, and occasionally Enterobacteriaceae.

• Adult Female Genital Tract:
    - Complex and constantly changing according to the menstrual cycle.
    - Dominant species: Acid-tolerant lactobacilli, specifically Lactobacillus acidophilus (Döderlein’s bacilli).
    - Mechanism: Lactobacilli ferment glycogen from the vaginal epithelium into lactic acid, maintaining a protective acidic pH of $4.0$ to $4.6$.
    - Other residents: Peptostreptococcus, Clostridium, Bacteroides, Candida, and Gardnerella vaginalis.

Pathogenicity and Host Defense

• Microbial Antagonism: Normal microbiota compete with and prevent pathogens from establishing infection.

• Opportunistic Pathogens: Harmless residents that cause disease when introduced to new sites or when host immunity is compromised.
    - Example: Viridans group streptococci are common in the upper respiratory tract. If introduced to the bloodstream (e.g., during dental work), they can settle on heart valves and cause endocarditis.

• Immunity: Derived from the Latin "immunis" (free of burden); the general ability of a host to resist infection or disease.