Human microbiome

The human microbiome (or human microbiota) is the assemblage of microorganisms that reside on the surface and in deep layers of skin, in the saliva and oral mucosa, in the conjunctiva, and in the gastrointestinal tracts. They include bacteria, fungi, and archaea. Some of these organisms perform tasks that are useful for the human host. However, the majority have no known beneficial or harmful effect. Those that are expected to be present, and that under normal circumstances do not cause disease, but instead participate in maintaining health, are deemed members of the normal flora. Though widely known as "microflora", this is, in technical terms, a misnomer, since the word root "flora" pertains to plants, and biota refers to the total collection of organisms in a particular ecosystem. Recently, the more appropriate term "microbiota" is applied, though its use has not eclipsed the entrenched use and recognition of "flora" with regard to bacteria and other microorganisms. Both terms are being used in different literature. Studies in 2009 questioned whether the decline in biota (including microfauna) as a result of human intervention might impede human health^[1]

Bacteria

Populations of microbes (such as bacteria and yeasts) inhabit the skin and mucosa. Their role forms part of normal, healthy human physiology, however if microbe numbers grow beyond their typical ranges (often due to a compromised immune system) or if microbes populate atypical areas of the body (such as through poor hygiene or injury), disease can result.

It is estimated that 500 to 1000 species of bacteria live in the human gut^[2] and a roughly similar number on the skin.^[3][4] Bacterial cells are much smaller than human cells, and there are at least ten times as many bacteria as human cells in the body (approximately 10¹⁴ versus 10¹³).^[5][6] Though members of the flora are found on all surfaces exposed to the environment (on the skin and eyes, in the mouth, nose, small intestine), the vast majority of bacteria live in the large intestine.

Many of the bacteria in the digestive tract, collectively referred to as the gut flora, are able to break down certain nutrients such as carbohydrates that humans otherwise could not digest. The majority of these commensal bacteria are anaerobes, meaning they survive in an environment with no oxygen. Normal flora bacteria can act as opportunistic pathogens at times of lowered immunity.^[7]

Escherichia coli (a.k.a. E. coli) is a bacterium that lives in the colon; it is an extensively studied model organism and probably the best-understood bacterium of all.^[8] Certain mutated strains of these gut bacteria do cause disease; an example is E. coli O157:H7.

A number of types of bacteria, such as Actinomyces viscosus and A. naeslundii, live in the mouth, where they are part of a sticky substance called plaque. If this is not removed by brushing, it hardens into calculus (also called tartar). The same bacteria also secrete acids that dissolve tooth enamel, causing tooth decay.

The vaginal microflora consist mostly of various lactobacillus species. It was long thought that the most common of these species was Lactobacillus acidophilus, but it has later been shown that the most common one is L. iners followed by L. crispatus. Other lactobacilli found in the vagina are L. delbruekii and L. gasseri. Disturbance of the vaginal flora can lead to bacterial vaginosis.

Archaea

Archaea are present in the human gut, but, in contrast to the enormous variety of bacteria in this organ, the numbers of archaeal species are much more limited.^[9] The dominant group are the methanogens, particularly Methanobrevibacter smithii and Methanosphaera stadtmanae.^[10] However, colonization by methanogens is variable, and only about 50% of humans have easily-detectable populations of these organisms.^[11]

As of 2007, no clear examples of archaeal pathogens are known,^[12][13] although a relationship has been proposed between the presence of some methanogens and human periodontal disease.^[14]

Fungal flora

Fungi, in particular yeasts, are present in the human gut. The best-studied of these are Candida species. This is because of their ability to become pathogenic in immunocompromised hosts.^[15] Yeasts are also present on the skin, particularly Malassezia species, where they consume oils secreted from the sebaceous glands.^[16][17]

Flora by anatomical area

Main article: List of human flora

Skin flora

Main article: Skin flora

A study of 20 skin sites on each of 10 healthy humans found 205 identified genera in nineteen bacterial phyla, with most sequences assigned to four phyla: Actinobacteria (51.8%), Firmicutes (24.4%), Proteobacteria (16.5%), and Bacteroidetes (6.3%).^[18]

Conjunctival flora

These are sparse in occurrence, but Gram-positive cocci and Gram-negative rods are present.^[19]

A small number of bacteria are normally present in the conjunctiva. Staphylococcus epidermidis and certain coryneforms such as Propionibacterium acnes are dominant. Staphylococcus aureus, streptococci, Haemophilus sp. and Neisseria sp. sometimes occur. The lachrymal glands continuously secrete, keeping the conjunctiva moist, while intermittent blinking lubricates the conjunctiva and washes away foreign material. Tears contain bactericides such as lysozyme, so that microorganisms have difficulty in surviving the lysozyme and settling on the epithelial surfaces.

Some pathogens able to infect the conjunctiva, such as Neisseria gonorrhoeae and Chlamydia trachomatis are thought to have special processes allowing them to attach to the conjunctival epithelium. Newborn infants are particularly prone to bacterial attachment. Chlamydia and Neisseria may be present in an infected mother and show up on the cervical and vaginal epithelium - in such cases the newborn's eyes may be treated with silver nitrate or antibiotics.

Gut flora

Main article: Gut flora

The gut flora is the human flora of microorganisms that normally live in the digestive tract and can perform a number of useful functions for their hosts. The average human body, consisting of about 10¹³ (10,000,000,000,000 or about ten trillion) cells, has about ten times that number of microorganisms in the gut.^{[20][21][22][23]} The metabolic activity performed by these bacteria is equal to that of a virtual organ, leading to gut bacteria being termed a "forgotten" organ.^[24]

Bacteria make up most of the flora in the colon^[25] and 60% of the dry mass of feces.^[22] This fact makes feces an ideal source to test for gut flora for any tests and experiments by extracting the nucleic acid from fecal specimens, and bacterial 16S rRNA gene sequences are generated with bacterial primers. This form of testing is also often preferable to more invasive techniques, such as biopsies. Somewhere between 300^[22] and 1000 different species live in the gut,^[20] with most estimates at about 500.^[23][26] However, it is probable that 99% of the bacteria come from about 30 or 40 species.^[27] Fungi and protozoa also make up a part of the gut flora, but little is known about their activities.

Research suggests that the relationship between gut flora^[28] and humans is not merely commensal (a non-harmful coexistence), but rather is a mutualistic, symbiotic relationship.^[20] Though people can survive with no gut flora,^[23] the microorganisms perform a host of useful functions, such as fermenting unused energy substrates, training the immune system, preventing growth of harmful species,^[22] regulating the development of the gut, producing vitamins for the host (such as biotin and vitamin K), and producing hormones to direct the host to store fats. However, in certain conditions, some species are thought to be capable of causing disease by causing infection or increasing cancer risk for the host.^[22][25]

Some bacteria found in the large intestine of humans:

Bacterium	Range of Incidence
Bacteroides fragilis	100
Bacteroides melaninogenicus	100
Bacteroides oralis	100
Lactobacillus	20-60
Clostridium perfringens	25-35
Clostridium septicum	5-25
Clostridium tetani	1-35
Bifidobacterium bifidum	30-70
Staphylococcus aureus	30-50
Enterococcus faecalis	100
Escherichia coli	100
Salmonella enteritidis	3-7
Klebsiella sp.	40-80
Enterobacter sp.	40-80
Proteus mirabilis	5-55
Pseudomonas aeruginosa	3-11
Peptostreptococcus sp.	?common
Peptococcus sp.	?common

^[29]

Vaginal flora

Main article: Vaginal flora

Oral cavity

Main article: Oral microbiology

See also

• Microorganism
• Human microbiome project
• Drug resistance

References

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19. ^ The Normal Bacterial Flora of Humans
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25. ^ ^{a b} University of Glasgow. 2005. The normal gut flora. Available through web archive. Accessed May 22, 2008
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28. ^ Gut flora are also known as gut microbiota.
29. ^ Normal Bacterial Flora of Humans