Microbe Ecosystems of the Body

The human microbiota consists of the entire collection of microbes that live in and on the body. In fact, there are 10 times as many microbial inhabitants of the body than there are body cells. Study of the human microbiome is inclusive of inhabitant microbes as well as the entire genomes of the body's microbial communities. These microbes reside in distinct locations in the ecosystem of the human body and perform important functions that are necessary for healthy human development. For example, gut microbes enable us to properly digest and absorb nutrients from the foods we eat. Gene activity of the beneficial microbes that colonize the body impact human physiology and protect against pathogenic microbes. Disruption in the proper activity of the microbiome has been associated with the development of a number of autoimmune diseases including diabetes and fibromyalgia.

Microbes of the Body

Microscopic organisms that inhabit the body include archaea, bacteria, fungi, protists, and viruses. Microbes start to colonize the body from the moment of birth. An individual's microbiome changes in number and type throughout his or her lifetime, with the numbers of species increasing from birth to adulthood and decreasing in old age. These microbes are unique from person to person and can be impacted by certain activities, such as hand washing or taking antibiotics. Bacteria are the most numerous microbes in the human microbiome.

  • Archaea - single-celled prokaryotes that are capable of living in some of the most extreme environments. They were once thought to be bacteria, but were found to differ from bacteria in cell wall composition and rRNA type. Archaeans can be found in the human gut and include methanogen species, which require oxygen free conditions in order to survive.
  • Bacteria - single-celled prokaryotes with a variety of species and shapes. These diverse microbes are capable of inhabiting a number of different environments and can be found in various areas of the body including on the skin, inside the digestive tract, and inside the female reproductive tract.
  • Fungi - unicellular (yeasts and molds) and multicellular organisms (mushrooms) that contain spore-producing fruit bodies for reproduction. They don't perform photosynthesis; they instead acquire their nutrients by absorption. The fungal communities of the body are also called the mycobiome. Unicellular yeast colonize areas of the body such as the skin, vagina, and gastrointestinal tract.
  • Protists - diverse group of eukaryotes that may be unicellular or multicellular. Many protists don't share common characteristics but are grouped together because they are not animalsplants, or fungi. Examples of protists include amoebas, paramecia, and sporozoans. While many protists are parasitic to their hosts, others exist in commensalistic (one species benefits without harming or helping the other) or mutualistic relationships (both species benefit). Protists that commonly reside as part of the microbiome of the human gut include Blastocystis and Enteromonas hominis.
  • Viruses - infectious particles consisting of genetic material (DNA or RNA) enclosed within a protein coat called a capsid. A number of viruses are a part of the human microbiome and are inclusive of viruses that infect human cells, viruses that infect bacteria (bacteriophages), and viral gene segments that have been inserted into human chromosomes. The human virome resides in several areas of the body including the gastrointestinal tract, mouth, respiratory tract, and the skin.

The human microbiome also includes microscopic animals, such as mites. These tiny arthropods typically colonize the skin, belong to the class Arachnida, and are related to spiders.

Skin Microbiome

Bacteria in Sweat Gland Pore
Illustration of bacteria around a sweat gland pore on the surface of human skin. Sweat pores bring sweat from a sweat gland to the skin surface. The sweat evaporates, removing heat and playing a vital role in cooling the body and preventing it from overheating. Bacteria around the pores metabolize organic substances secreted in the sweat into odorous substances. Juan Gaertner/Science Photo Library/Getty Images

Human skin is populated by a number of different microbes that reside on the surface of the skin, as well as within glands and hair. Our skin is in constant contact with our external environment and serves as the body's first line of defense against potential pathogens. Skin microbiota help to prevent pathogenic microbes from colonizing the skin by occupying skin surfaces. They also help to educate our immune system by alerting immune cells to the presence of pathogens and initiating an immune response. The ecosystem of the skin is very diverse, with different types of skin surfaces, acidity levels, temperature, thickness, and exposure to sunlight. As such, microbes that inhabit a particular location on or within the skin are different from microbes from other skin locals. For example, microbes that populate areas that are typically moist and hot, such as under the arm pits, are different from microbes that colonize the drier, cooler surfaces of the skin found in areas such as on the arms and legs. Commensal microbes that typically colonize the skin include bacteria, viruses, fungi, and animal microbes, such as mites.

Bacteria that colonize the skin thrive in one of the three main types of skin environments: oily, moist, and dry. The three main species of bacteria that populate these areas of the skin are Propionibacterium (found predominately in the oily areas), Corynebacterium (found in moist areas), and Staphylococcus (found in dry areas). While most of these species are not harmful, they may become harmful under certain conditions. For example, Propionibacterium acnes species live on oily surfaces such as the face, neck, and back. When the body produces excess amounts of oil, these bacteria proliferate at a high rate. This excessive growth can lead to the development of acne. Other species of bacteria, such as Staphylococcus aureus and Streptococcus pyogenes, can cause more serious problems. Conditions caused by these bacteria include septicemia and strep throat (S. pyogenes).

Not much is know about commensal viruses of the skin as research in this area has been limited so far. Viruses have been found to reside on skin surfaces, within sweat and oil glands, and inside skin bacteria. Species of fungi that colonize the skin include Candida, Malassezia, Cryptocoocus, Debaryomyces, and Microsporum. As with bacteria, fungi that proliferate at an unusually high rate can cause problematic conditions and disease. Malassezia species of fungi can cause dandruff and atopic eczema. Microscopic animals that colonize the skin include mites. Demodex mites, for example, colonize the face and live inside hair follicles. They feed on oil secretions, dead skin cells, and even on some skin bacteria.

Gut Microbiome

E. coli Bacteria
Colored scanning electron micrograph (SEM) of Escherichia coli bacteria. E. coli are Gram-negative rod-shaped bacteria that are part of the normal flora of the human gut. Steve Gschmeissner/Science Photo Library/Getty Images

The human gut microbiome is diverse and dominated by trillions of bacteria with as many as one-thousand different bacterial species. These microbes thrive in the harsh conditions of the gut and are heavily involved in maintaining healthy nutrition, normal metabolism, and proper immune function. They aid in the digestion of non-digestible carbohydrates, the metabolism of bile acid and drugs, and in the synthesis of amino acids and many vitamins. A number of gut microbes also produce antimicrobial substances that protect against pathogenic bacteria. Gut microbiota composition is unique to each person and does not stay the same. It changes with factors such as age, dietary changes, exposure to toxic substances (antibiotics), and changes in heath. Alterations in the composition of commensal gut microbes has been associated with the development of gastrointestinal diseases, such as inflammatory bowel disease, celiac disease, and irritable bowel syndrome. The vast majority of bacteria (around 99%) that inhabit the gut come primarily from two phyla: Bacteroidetes and Firmicutes. Examples of other bacteria types found in the gut include bacteria from the phyla Proteobacteria (Escherichia, Salmonella, Vibrio), Actinobacteria, and Melainabacteria.

Gut microbiome also includes archaea, fungi, and viruses. The most abundant archaeans in the gut include the methanogens Methanobrevibacter smithii and Methanosphaera stadtmanae. Species of fungi that inhabit the gut include Candida, Saccharomyces and Cladosporium. Alterations in the normal composition of gut fungi have been associated with the development of diseases such as Crohn's disease and ulcerative colitis. The most abundant viruses in the gut microbiome are bacteriophages that infect commensal gut bacteria.

Mouth Microbiome

Dental Plaque
Colored scanning electron micrograph (SEM) of dental plaque (pink) on a tooth. Plaque consists of a film of bacteria embedded in a glycoprotein matrix. The matrix is formed from bacterial secretions and saliva. Steve Gschmeissner/Science Photo Library/Getty Images

Microbiota of the oral cavity number in the millions and include archaea, bacteria, fungi, protists, and viruses. These organisms exist together and most in a mutualistic relationship with the host, where both the microbes and the host benefit from the relationship. While the majority of oral microbes are beneficial, preventing harmful microbes from colonizing the mouth, some have been known to become pathogenic in response to environmental changes. Bacteria are the most numerous of the oral microbes and include Streptococcus, Actinomyces, Lactobacterium, Staphylococcus, and Propionibacterium. Bacteria protect themselves from stressful conditions in the mouth by producing a sticky substance called biofilm. Biofilm protects bacteria from antibiotics, other bacteria, chemicals, tooth brushing, and other activities or substances that are hazardous to the microbes. Biofilms from different bacterial species form dental plaque, which adheres to tooth surfaces and can cause tooth decay.

Oral microbes often cooperate with one another for the benefit of the microbes involved. For example, bacteria and fungi sometimes exist in mutualistic relationships that can be harmful to the host. The bacterium Streptococcus mutans and fungus Candida albicans working in conjunction cause severe cavities, most often seen in preschool aged individuals. S. mutans produces a substance, extracellular polysaccharide (EPS), that allows the bacterium to stick to teeth. EPS is also used by C. albicans to produce a glue-like substance that enables the fungus to stick to teeth and to S. mutans. The two organisms working together lead to greater plaque production and increased acid production. This acid destroys tooth enamel, resulting in tooth decay.

Archaea found in the oral microbiome include the methanogens Methanobrevibacter oralis and Methanobrevibacter smithii. Protists that inhabit the oral cavity include Entamoeba gingivalis and Trichomonas lenax. These commensal microbes feed on bacteria and food particles and are found in much greater numbers in individuals with gum disease. The oral virome predominantly consists of bacteriophages.


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