Skin flora

The skin flora, more properly referred to as the skin microbiome or skin microbiota, are the microorganisms which reside on the skin. Most research has been upon those that reside upon the 2 square metres of human skin, cf. the human microbiome. Many of them are bacteria of which there are around 1000 species upon human skin from 19 phyla. The total number of bacteria on an average human has been estimated at 1012 (1 trillion). 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 commensals (are not harmful to their host) or mutualistic (offer a benefit). The benefits bacteria can offer include preventing transient pathogenic organisms from colonizing the skin surface, either by competing for nutrients, secreting chemicals against them, or stimulating the skin's immune system. However, resident microbes can cause skin diseases and enter the blood system creating life-threatening diseases particularly in immunosuppressed people. 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.

Bacteria


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.

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. 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%).

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.

Fungal
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.

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.

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

The Belly Button Biodiversity Project began at North Carolina State University in early 2011 with two initial groups of 35 and 25 volunteers. 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  that contained a 0.5 ml 10% phosphate saline buffer. Researchers at North Carolina State University, led by Jiri Hulcr, 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). These samples then were analyzed using 16S rDNA libraries so that strains that did not grow well in cultures could be identified.

The researchers at North Carolina State University discovered that while it was difficult to predict every strain of bacteria in the microbiome of the belly button that they could predict which strains would be prevalent and which strains of bacteria would be quite rare in the microbiome. It was found that the navel or belly button microbiomes only contained a few prevalent types of bacteria (Staphylococcus, Corynebacterium, Actinobacteria, Clostridiales, and Bacilli) and many different types of rare bacteria. 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 that he/she had not bathed or showered for many years.

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 (of which the Belly Button Biodiversity Project is a part). (In these larger studies it has been found that females generally have more Staphylococcus living in their skin microbiomes (usually Staphylococcus epidermidis) and that men have more Corynebacterium living in their skin microbiomes.) According to the Belly Button Biodiversity Project at North Carolina State University, there are two types of microorganisms found in the belly button and surrounding areas. Transient bacteria(bacteria that does not reproduce)   forms  the majority of the organisms found in the belly button, and an estimated 1400 various strains were found in 95% of participants of the study.

The Belly Button Biodiversity Project is ongoing and has now taken swabs from over 500 people. The project was designed to take away the idea that bacteria is always harmful to humans and that humans are at war with bacteria  (since most strains of bacteria are harmless   if not beneficial for the human body ) and it was also designed to create public interest in microbiology. The project is also working with the Human Microbiome Project to help see the connections between our microbiomes and age, sex, ethnicity, location and our health.

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. 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. 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. It can also inhibit the growth of Helicobacter pylori. 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."

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:
 * Propionibacteria in adolescent and adult sebaceous glands can turn its amino acids into propionic acid.
 * Staphylococcus epidermidis creates body odor by breaking sweat into isovaleric acid (3-methyl butanoic acid).
 * Bacillus subtilis creates strong foot odor.

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.

Acidity
The superficial layers of the skin are naturally acidic (pH 4-4.5) due to lactic acid in sweat and produced by skin bacteria. 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. Another factor affecting the growth of pathological bacteria is that the antimicrobial substances secreted by the skin are enhanced in acidic conditions. 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.

Immune system
If activated, the immune system in the skin produces cell-mediated immunity against microbes such as dermatophytes (skin fungi). 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. The shedding of skin is a general means to control the build up flora upon the skin surface.

Skin diseases
Microorganisms play a role in noninfectious skin diseases such as atopic dermatitis, rosacea, psoriasis, and acne Damaged skin can cause nonpathogenic bacteria to become pathogenic.

Infected devices
Skin microbes are source of infected medical devices such as catheters.

Hygiene
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)

Contagion
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.

Removal
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.

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.

An important use of hand washing is to prevent the transmission of antibiotic resistant skin flora that cause hospital-acquired infections such as Methicillin-resistant Staphylococcus aureus. While such flora have become antibiotic resistant due to antibiotics there is no evidence that recommended antiseptics or disinfectants selects for antibiotic-resistant organisms when used in hand washing. However, many strains of organisms are resistant to some of the substances used in antibacterial soaps such as Triclosan.

One survey of bar soaps in dentist clinics found they all had their own flora and on average from two to five different genera of microorganisms with those used most more likely to have more species varieties. Another survey of bar soaps in public toilets found even more flora. Another study found that very dry soaps are not infected while all are that rest in pools of water. However, research upon soap that was specially infected found that soap flora do not transmit to the hands.

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, dermatitis provoked by microorganisms and 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.

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.

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. 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.

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