Infection, Infectious Disease, and Epidemiology: The Human Microbiome and Symbiotic Relationships

Infection, Infectious Disease, and Epidemiology

The Human Microbiome and Microbiota

The human microbiome encompasses all the microorganisms that colonize the human body without normally causing disease. The term microbiota refers specifically to the actual organisms present. These microbes play essential roles in health and disease, and their composition is influenced by various factors.

• Resident microbiota: Microbes that are consistently present on or in the body throughout life.

• Transient microbiota: Microbes that temporarily colonize the body but do not persist long-term.

Types of Symbiotic Relationships

Microorganisms interact with their human host in different types of symbiotic relationships. These relationships can be classified based on the effects on both the microbe and the host.

Type	Organism 1	Organism 2	Example
Mutualism	Benefits	Benefits	Bacteria in human colon
Commensalism	Benefits	Neither benefits nor is harmed	Mites in human hair follicles
Amensalism	Is harmed	Neither benefits nor is harmed	Fungus secreting an antibiotic, inhibiting nearby bacteria
Parasitism	Benefits	Is harmed	Tuberculosis bacteria in human lung

• Mutualism: Both organisms benefit (e.g., bacteria in the human colon produce vitamins and receive nutrients).

• Commensalism: One organism benefits, the other is unaffected (e.g., Staphylococcus epidermidis on skin).

• Parasitism: One organism benefits at the expense of the other (e.g., tapeworms in the human colon).

• Amensalism: One organism is harmed, the other is unaffected (e.g., antibiotic-producing fungi inhibiting bacteria).

Acquisition of the Human Microbiota

The human body is colonized by microbes shortly after birth. The womb is typically a sterile environment, and colonization begins during and after delivery. The resident microbiota is established within the first few months of life.

• During birth: Exposure to maternal microbiota.

• First breaths and meals: Introduction of environmental and dietary microbes.

• Not in the womb: The fetus is generally free of microorganisms before birth.

Factors Influencing the Microbiome

Several factors can influence the composition and diversity of the human microbiome:

• Age

• Diet

• Physiological state

• Lifestyle and antibiotic use

• Body site (different regions support different communities)

Distribution of Microbes in the Human Body

The highest density of microbes is found in the gut, particularly the colon. Other body sites, such as the skin, mouth, and urogenital tract, also harbor distinct microbial communities.

Resident and Transient Microbiota

Resident microbiota are long-term inhabitants of the body, while transient microbiota are present only temporarily. Transient microbiota may be removed by the immune system or competition from resident microbes.

• Microorganisms that colonize the skin or mucosal surfaces for a limited period are called transient microbiota.

Opportunistic Pathogens

Normal microbiota can become opportunistic pathogens under certain conditions, causing disease when the opportunity arises. Factors that can lead to this include:

• Introduction of normal microbiota into an unusual site in the body

• Immune suppression

• Changes in the normal microbiome (e.g., due to antibiotics)

• Stressful or hormonal changes

Summary Table: Some Resident Microbiota

The following table summarizes the genera of resident microbiota found in various body sites and their notable characteristics.

Body Site	Genera	Notes
Upper Respiratory Tract	Staphylococcus, Streptococcus, Corynebacterium, Neisseria, Haemophilus, Mycoplasma, Fungi	The nose is cooler than the rest of the respiratory tract; contains unique microbiota. Microbes rarely cause disease unless immune system is compromised.
Upper Digestive Tract	Actinomyces, Bacteroides, Corynebacterium, Haemophilus, Lactobacillus, Neisseria, Staphylococcus, Treponema, Entamoeba	Microbes colonize surfaces of teeth, gingiva, lining of cheeks, and pharynx. Dozens of species live in large numbers.
Lower Digestive Tract	Bacteroides, Bifidobacterium, Clostridium, Enterococcus, Escherichia, Lactobacillus, Proteus, Shigella, Candida, Entamoeba, Trichomonas	Bacteria are mostly strict anaerobes, though some facultative anaerobes are also resident.
Female Urinary and Reproductive Systems	Lactobacillus, Streptococcus, Staphylococcus, Candida	Microbiota changes as acidity in the vagina changes during the menstrual cycle.
Male Urinary and Reproductive Systems	Staphylococcus, Streptococcus, Corynebacterium	Urine flow prevents colonization except in the distal portion of the urethra.
Eyes and Skin	Staphylococcus, Corynebacterium, Propionibacterium, Micrococcus, Candida, Malassezia	Microbiota live on the outer dead layers of the skin and in hair follicles and pores; tears wash most away from the eyes.

Key Concepts and Review Questions

• Mutualism is a relationship where both members benefit (e.g., bacteria in the colon).

• Humans acquire resident microbiota during birth, first breaths, and first meals, but not in the womb.

• Normal microbiota can become opportunistic pathogens due to immune suppression, stress, antibiotics, or hormonal changes.

• Transient microbiota are associated with the body for a limited amount of time.

Example: Staphylococcus epidermidis living on human skin is an example of commensalism or mutualism, depending on the context. Bacteria in the human colon typically represent mutualism, while tapeworms in the colon are parasitic.