Skin flora

Skin flora

Depiction of the human body and bacteria that predominate

The skin flora, more properly referred to as the skin microbiome or skin microbiota, are the human skin, cf. the human microbiome. Many of them are bacteria of which there are around 1000 species upon human skin from 19 phyla.[1][2] The total number of bacteria on an average human has been estimated at 1012 (1 trillion).[3] Most are found in the superficial layers of the epidermis and the upper parts of hair follicles.

Skin flora is usually non-pathogenic, and either colonizing the skin surface, either by competing for nutrients, secreting chemicals against them, or stimulating the skin's immune system.[4] However, resident microbes can cause skin diseases and enter the blood system creating life-threatening diseases particularly in immunosuppressed people.[4] Hygiene to control such flora is important in preventing the transmission of antibiotic resistant hospital-acquired infections.

A major nonhuman skin flora is Batrachochytrium dendrobatidis, a chytrid and non-hyphal zoosporic fungus that causes chytridiomycosis, an infectious disease thought to be responsible for the decline in amphibian populations.

Species variety


Scanning electron microscope image of Staphylococcus epidermidis one of roughly a thousand bacteria species present on human skin. Though usually not pathogenic, it can cause skin infections and even life-threatening illnesses in those that are immunocompromised.

The estimate of the number of species present on skin bacteria has been radically changed by the use of 16S ribosomal RNA to identify bacterial species present on skin samples direct from their genetic material. Previously such identification had depended upon microbiological culture upon which many varieties of bacteria did not grow and so were hidden to science.[1]

Staphylococcus epidermidis and Staphylococcus aureus were thought from cultural based research to be dominant. However 16S ribosomal RNA research finds that while common, these species make up only 5% of skin bacteria.[5] However, skin variety provides a rich and diverse habitat for bacteria. Most come from four phyla: Actinobacteria (51.8%), Firmicutes (24.4%), Proteobacteria (16.5%), and Bacteroidetes (6.3%).

ecology of the 20 sites on the skin studied in the Human Microbiome Project

There are three main ecological areas: sebaceous, moist, and dry. Propionibacteria and Staphylococci species were the main species in sebaceous areas. In moist places on the body Corynebacteria together with Staphylococci dominate. In dry areas, there is a mixture of species but b-Proteobacteria and Flavobacteriales are dominant. Ecologically, sebaceous areas had greater species richness than moist and dry one. The areas with least similarity between people in species were the spaces between fingers, the spaces between toes, axillae, and umbilical cord stump. Most similarly were beside the nostril, nares (inside the nostril), and on the back.[1]

Frequency of the best studied skin microbes[4]
Organism observations
Staphylococcus epidermidis Common, occasionally pathogenic
Staphylococcus aureus Infrequent, usually pathogenic
Staphylococcus warneri Infrequent, occasionally pathogenic
Streptococcus pyogenes Infrequent, usually pathogenic
Streptococcus mitis Frequent, occasionally pathogenic
Propionibacterium acnes Frequent, occasionally pathogenic
Corynebacterium spp. Frequent, occasionally pathogenic
Acinetobacter johnsonii Frequent, occasionally pathogenic
Pseudomonas aeruginosa Infrequent, occasionally pathogenic


A study of the area between toes in 100 young adults found 14 different genera of fungi. These include yeasts such as Candida albicans, Rhodotorula rubra, Torulopsis and Trichosporon cutaneum, dermatophytes (skin living fungi) such as Microsporum gypseum, and Trichophyton rubrum and nondermatophyte fungi (opportunistic fungi that can live in skin) such as Rhizopus stolonifer, Trichosporon cutaneum, Fusarium, Scopulariopsis brevicaulis, Curvularia, Alternaria alternata, Paecilomyces, Aspergillus flavus and Penicillium species.[6]

A study by the National Human Genome Research Institute in Bethesda, Maryland, researched the DNA of human skin fungi at 14 different locations on the body. These were the ear canal, between the eyebrows, the back of the head, behind the ear, the heel, toenails, between the toes, forearm, back, groin, nostrils, chest, palm, and the crook of the elbow. The study showed a large fungal diversity across the body, the richest habitat being the heel, which hosts about 80 species of fungi. By way of contrast, there are some 60 species in toenail clippings and 40 between the toes. Other rich areas are the palm, forearm and inside the elbow, with from 18 to 32 species. The head and the trunk hosted between 2 and 10 each.[7]

Umbilical microbiome

The umbilicus, or navel, is an area of the body that is rarely exposed to UV light, soaps, or bodily secretions[8] (the navel does not produce any secretions or oils) [9] and because it is an almost undisturbed community of bacteria [10] it is an excellent part of the skin microbiome to study.[11] The navel, or umbilicus is a moist microbiome of the body [12] (with high humidity and temperatures),[13] that contains a large amount of bacteria,[14] especially bacteria that favors moist conditions such as Corynebacterium[15] and Staphylococcus.[13]

The Belly Button Biodiversity Project began at North Carolina State University in early 2011 with two initial groups of 35 and 25 volunteers.[10] Volunteers were given sterile cotton swabs and were asked to insert the cotton swabs into their navels, to turn the cotton swab around three times and then return the cotton swab to the researchers in a vial [16] that contained a 0.5 ml 10% phosphate saline buffer.[10] Researchers at North Carolina State University, led by Jiri Hulcr,[17] then grew the samples in a culture until the bacterial colonies were large enough to be photographed and then these pictures were posted on the Belly Button Biodiversity Project’s website (volunteers were given sample numbers so that they could view their own samples online).[16] These samples then were analyzed using 16S rDNA libraries so that strains that did not grow well in cultures could be identified.[10]

The researchers at North Carolina State University discovered that while it was difficult to predict every strain of bacteria in the microbiome of the navel that they could predict which strains would be prevalent and which strains of bacteria would be quite rare in the microbiome.[10] It was found that the navel microbiomes only contained a few prevalent types of bacteria (Staphylococcus, Corynebacterium, Actinobacteria, Clostridiales, and Bacilli) and many different types of rare bacteria.[10] Other types of rare organisms were discovered inside the navels of the volunteers including three types of Archaea (an organism that usually lives in only extreme environments) and two of the three types of Archaea were found in one volunteer who claimed not to have bathed or showered for many years.[10]

Staphylococcus and Corynebacterium were among the most common types of bacteria found in the navels of this project’s volunteers and these types of bacteria have been found to be the most common types of bacteria found on the human skin in larger studies of the skin microbiome [18] (of which the Belly Button Biodiversity Project is a part).[10] (In these larger studies it has been found that females generally have more Staphylococcus living in their skin microbiomes [18] (usually Staphylococcus epidermidis) [16] and that men have more Corynebacterium living in their skin microbiomes.) [18] According to the Belly Button Biodiversity Project [10] at North Carolina State University, there are two types of microorganisms found in the navel and surrounding areas. Transient bacteria(bacteria that does not reproduce) [12] forms the majority of the organisms found in the navel, and an estimated 1400 various strains were found in 95% of participants of the study.[19]

The Belly Button Biodiversity Project is ongoing and has now taken swabs from over 500 people.[10] The project was designed with the aim of countering that misconception that bacteria are always harmful to humans [20] and that humans are at war with bacteria.[21] In actuality, most strains of bacteria are harmless [13] if not beneficial for the human body.[22] Another of the project's goals is to foster public interest in microbiology.[17] Working in concert with the Human Microbiome Project, the Belly Button Biodiversity Project also studies the connections between human microbiomes and the factors of age, sex, ethnicity, location[17] and overall health.[23]

Relationship to host

Skin microflora can be commensals, mutualistic or pathogens. Often they can be all three depending upon the strength of the person's immune system.[4] Research upon the immune system in the gut and lungs has shown that microflora aids immunity development: however such research has only started upon whether this is the case with the skin.[4] Pseudomonas aeruginosa is an example of a mutualistic bacterium that can turn into a pathogen and cause disease: if it gains entry into the blood system it can result in infections in bone, joint, gastrointestinal, and respiratory systems. It can also cause dermatitis. However, Pseudomonas aeruginosa produces antimicrobial substances such as pseudomonic acid (that are exploited commercially such as Mupirocin). This works against staphylococcal and streptococcal infections. Pseudomonas aeruginosa also produces substances that inhibit the growth of fungus species such as Candida krusei, Candida albicans, Torulopsis glabrata, Saccharomyces cerevisiae and Aspergillus fumigatus.[24] It can also inhibit the growth of Helicobacter pylori.[25] So important is its antimicrobial actions that it has been noted that "removing P. aeruginosa from the skin, through use of oral or topical antibiotics, may inversely allow for aberrant yeast colonization and infection."[4]

Another aspect of bacteria is the generation of body odor. Sweat is odorless however several bacteria may consume it and create byproducts which may be considered putrid by man (as in contrast to flies, for example, that may find them attractive/appealing). Several examples are:

Skin defenses

Antimicrobial peptides

The skin creates antimicrobial peptides such as cathelicidins that control the proliferation of skin microbes. Cathelicidins not only reduce microbe numbers directly but also cause the secretion of cytokine release which induces inflammation, angiogenesis, and reepithelialization. Conditions such as atopic dermatitis have been linked to the suppression in cathelicidin production. In rosacea abnormal processing of cathelicidin cause inflammation. Psoriasis has been linked to self-DNA created from cathelicidin peptides that causes autoinflammation. A major factor controlling cathelicidin is vitamin D3.[28]


The superficial layers of the skin are naturally acidic (pH 4-4.5) due to lactic acid in sweat and produced by skin bacteria.[29] At this pH mutualistic flora such as Staphylococci, Micrococci, Corynebacterium and Propionibacteria grow but not transient bacteria such as Gram negative bacteria like Escherichia and Pseudomonas or Gram positive ones such as Staphylococcus aureus or Candida albicans.[29] Another factor affecting the growth of pathological bacteria is that the antimicrobial substances secreted by the skin are enhanced in acidic conditions.[29] In alkaline conditions, bacteria cease to be attached to the skin and are more readily shed. It has been observed that the skin also swells under alkaline conditions and opens up allowing move to the surface.[29]

Immune system

If activated, the immune system in the skin produces cell-mediated immunity against microbes such as dermatophytes (skin fungi).[30] One reaction is to increase stratum corneum turnover and so shed the fungus from the skin surface. Skin fungi such as Trichophyton rubrum have evolved to create substances that limit the immune response to them.[30] The shedding of skin is a general means to control the buildup of flora upon the skin surface.


Skin diseases

Microorganisms play a role in noninfectious skin diseases such as atopic dermatitis,[31] rosacea, psoriasis,[32] and acne[33] Damaged skin can cause nonpathogenic bacteria to become pathogenic.[34]

Infected devices

Skin microbes are source of infected medical devices such as catheters.[35]


It is important to note that the human skin is host to numerous bacterial and fungal species, some of which are known to be harmful, some known to be beneficial and the vast majority unresearched. The use of bactericidal and fungicidal soaps will inevitably lead to bacterial and fungal populations which are resistant to the chemicals employed. (see Drug resistance)


Skin flora do not readily pass between people: 30 seconds of moderate friction and dry hand contact results in a transfer of only 0.07% of natural hand flora from naked with a greater percentage from gloves.[36]


The most effective (60 to 80% reduction) antimicrobial washing is with ethanol, isopropanol, and n-propanol. Viruses are most affected by high (95%) concentrations of ethanol, while bacteria are more affected by n-propanol.[37]

Unmedicated soaps are not very effective as illustrated by the following data. Health care workers washed their hands once in nonmedicated liquid soap for 30 seconds. The students/technicians for 20 times.[38]
Skin flora upon two hospital groups in colony-forming units per mL.
group and hand skin condition unwashed washed
Health care workers healthy 3.47 3.15
Health care workers damaged 3.33 3.29
Students/technicians healthy 4.39 3.54
Students/technicians damaged 4.58 4.43

An important use of Triclosan.[39]

One survey of [40] Another survey of bar soaps in public toilets found even more flora.[41] Another study found that very dry soaps are not infected while all are that rest in pools of water.[42] However, research upon soap that was specially infected found that soap flora do not transmit to the hands.[43]

Damaged skin

Washing skin repeatedly can damage the protective external layer and cause transepidermal loss of water. This can be seen in roughness characterized by scaling and dryness, itchiness, allergens penetrating the corneal layer and redness. Wearing gloves can cause further problems since it produces a humid environment favoring the growth of microbes and also contains irritants such as latex and talcum powder.[44]

Hand washing can damage skin because the stratum corneum top layer of skin consists of 15 to 20 layers of keratin disks, corneocytes, each of which is each surrounded by a thin film of skin lipids which can be removed by alcohols and detergents.[45]

Damaged skin defined by extensive cracking of skin surface, widespread reddening or occasional bleeding has also been found to be more frequently colonized by Staphylococcus hominis and these were more likely to methicillin resistant.[44] Though not related to greater antibiotic resistance, damaged skin was also more like to be colonized by Staphylococcus aureus, gram-negative bacteria, Enterococci and Candida.[44]

Comparison with other flora

The skin flora is different from that of the gut which is predominantly Firmicutes and Bacteroidetes.[46] There is also low level of variation between people that is not found in gut studies.[5] Both gut and skin flora however lack the diversity found in soil flora.[1]

See also


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  2. ^ Pappas S. (2009). Your Body Is a Wonderland ... of Bacteria. ScienceNOW Daily News
  3. ^ Todar K. Normal Bacterial Flora of Humans Todar's Online Textbook of Bacteriology.
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  5. ^ a b Grice EA, Kong HH, Renaud G, Young AC; NISC Comparative Sequencing Program, Bouffard GG, Blakesley RW, Wolfsberg TG, Turner ML, Segre JA (2008). "A diversity profile of the human skin microbiota". Genome Res 18 (7): 1043–50.  
  6. ^ Oyeka CA, Ugwu LO (2002). "Fungal flora of human toe webs". Mycoses 45 (11-12): 488–91.  
  7. ^ BBC News item
  8. ^ Ecological Society of America (2011-08-04). "Bellybutton microbiomes: Ecological research on the human biome" (Press Release). ScienceDaily. Retrieved 2013-04-20. 
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  14. ^ Kaplan, Karen (6/1/2009). "Study shows you're covered in bacteria - live with it.". The Star. Retrieved 2013-09-29. 
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  41. ^ Kabara JJ, Brady MB (1984). "Contamination of bar soaps under "in-use" conditions". J Environ Pathol Toxicol Oncol 5 (4-5): 1–14.  
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External links

  • Cellulitis Skin Infection
  • Human microbiome project
  • Todar's Online Textbook of Bacteriology