Normal Flora of the Skin-Skin Microbiome

Human skin is home to billions of diverse bacteria, archaea, fungi, and viruses, with bacteria making up the vast majority. Typically, a person has around 1,000 species of bacteria on their skin. The skin microbiome is seeded at birth. Most microorganisms live in the stratum corneum’s superficial layers and the hair follicles’ upper parts. Some microorganisms, however, reside in the deeper areas of the hair follicles. A variety of aerobic bacteria, anaerobic bacteria, and fungi inhabit these regions.

Schematic of skin histology viewed in cross-section with microorganisms and skin appendages (image source)

Skin surface varies greatly in chemical composition and moisture content. Generally, the skin surface is not a favorable place for microbial growth, as it is dry, salty, and poor in nutrients. subject to periodic drying but human skin is not uniform, it provides various micro-environments. Someone has aptly compared it with geographic regions of the earth; the desert of the forearm, the cool woods of the scalp, and the tropical forest of the armpit.

Residential microbial populations are higher in moist and warm areas of the skin such as axilla, perineum, and interdigital spaces of the toes. Availability of nutrients is another major factor that alters the quantity and diversity of microflora in a particular niche. Several kinds of sweat glands (such as eccrine glands, apocrine glands, and sebaceous glands) present in the skin secret secretions rich in microbial nutrients. The distribution of sweat glands on skin surfaces and differences in the composition of their secretions also affect the nature of skin flora.

Do you know?

Sweat itself does not smell, bacteria on your skin are the culprits for your body odor. Underarm odor develops as a result of bacterial activity on the secretions of the apocrine glands.

Types of Skin Flora

The microorganisms of the normal flora of the skin are either transient or residents.

  1. Transient microflora: Skin is the largest and most exposed organ so it is continually being inoculated with microorganisms. Most of these organisms can’t multiply and ultimately die either because of low moisture content or low pH on the skin surface.
  2. Resident microflora: Resident microorganisms are able to multiply, not merely survive, on the skin. The normal flora of the skin consists primarily of gram-positive bacteria.

Traditionally, skin flora were identified by use of culture-based methods, which used to favor easily culturable organisms and fail to capture the complete diversity of the microbiome. To circumvent this problem, nowadays, sequencing methods ( 16S ribosomal RNA gene sequencing for bacteria) are used to enumerate skin microbiota.

Gram-positive bacteria

Gram-positive bacteria are predominant members of the skin microbiome as they are better adapted to the dry conditions of the skin. These include Staphylococci, Micrococci, and a variety of both aerobic and anaerobic corynebacteria. Cutibacterium acnes (formerly Propionibacterium acnes) start colonizing after a child reaches the age of 10. It is ordinarily a harmless resident but certain strains can contribute to acne at puberty.

Gram-negative bacteria

Gram-negative bacteria are minor constituents of the skin flora as they can’t compete with gram-positive organisms. They are seen mostly in moist intertriginous areas, such as the toe webs and axilla. Predominant Gram-negative bacteria found on the skin are Acinetobacter, E. coli, Klebsiella, Enterobacter, and Proteus.

Fungi (molds/yeasts)

Yeasts are uncommon on the skin surface, but the lipophilic yeast Malassezia furfur is occasionally found on the scalp. Opportunistic fungal pathogen, Candida albicans is a member of the normal microflora of the skin. Malassezia spp., Aspergillus spp., Cryptococcus sp., Rhodotorula sp. are mostly food on foot regions.

Factors Affecting Skin Flora

Although the resident microflora on an individual’s skin remains relatively constant, various factors can affect the nature and extent of the normal flora:

  1. Change in weather conditions and exposure to sunlight alters the temperature and humidity of the skin thus altering the number and diversity of skin microflora. Exposure to UV radiation kills the normal flora.
  2. Individual’s health, age, and gender determine the type and the density of skin flora.
    Age-related changes in skin structure and function alter the microflora of the skin. For example, young children have a more varied microflora and carry more gram-negative bacteria and potential pathogens than adults.
  3. Personal hygienic habits influence the resident microflora. Unclean individuals usually have higher microbial population densities on their skin. Bathing or showering cleans the skin by the mechanical removal of bacteria shed on corneocytes but the resident microflora are replenished immediately. Bacteria living in the deeper areas of the hair follicles act as a reservoir for recolonization after the surface bacteria are removed.
  4. Host genotype, lifestyle, and pathophysiology also alters the normal skin flora.
Factors affecting variation in the skin microbiome

Factors contributing to variation in the skin microbiome (image source)

Beneficial roles of Skin Flora

  1. A barrier to infection: Skin is colonized by beneficial microorganisms that suppress the growth of pathogens by outcompeting them for space and food. For example, when the normal flora is inhibited by antibiotics, overgrowth of fungi such as C. albicans can occur.
    1. Cutibacterium acnes digest the oily substances from the sebaceous gland to create an acidic environment that makes it hard for the pathogen to colonize.
    2. S. epidermidis produces antimicrobial peptides and also stimulates antimicrobial peptide production by keratinocytes, which may provide protection against pathogenic bacteria.
    3. S. epidermidis produce chemicals that help reinforce the tight junctions between skin cells and protect the skins’ physical integrity.
  2. Immunological defenses: Shortly after birth, S. epidermidis communicates with regulatory T cells effectively training the immune system to tolerate commensal skin microbes while remaining alert against invaders. It boosts innate immune responses against intracellular bacteria.

When the balance is broken

  1. Opportunistic Infections: Skin normal flora can cause disease when they gain access to sterile sites such as tissues or blood.
    1. Surgical-wound infections: Surgical-wound infections are commonly associated with skin flora including various staphylococci and streptococci and Cutibacterium acnes.
    2. Osteomyelitis: Staphylococcus aureus is the most common bacterial cause of acute osteomyelitis in children and adults. Staphylococcus epidermidis and Cutibacterium acnes can cause osteomyelitis in patients with hip or knee prostheses as they enter the bloodstream at the site of skin wound or intravenous catheter.
    3. Endocarditis: S. aureus is the prominent cause of right-sided endocarditis in intravenous drug abusers. It is found that skin flora enter venous blood at the site of needle inoculation. Similarly, in people with prosthetic heart valve transplants, S. epidermidis is the major cause of endocarditis.
  2. Contaminants in blood culture: If disinfection is not done properly while drawing blood for culture, normal skin flora may grow in blood culture. S. epidermidis is one of such contaminants in diagnostic laboratories.

References and further readings

  1. Byrd, A. L., Belkaid, Y., & Segre, J. A. (2018). The human skin microbiome. Nature Reviews Microbiology, 16(3), 143–155.
  2. Davis, C. P. (1996). Normal Flora. In S. Baron (Ed.), Medical Microbiology (4th ed.). University of Texas Medical Branch at Galveston.
  3. Grice, E. A., & Segre, J. A. (2011). The skin microbiome. Nature Reviews. Microbiology, 9(4), 244–253.
  4. Eisenstein, M. (2020). The skin microbiome. Nature, 588(7838), S209–S209.
  5. Pastar, I., O’Neill, K., Padula, L., Head, C. R., Burgess, J. L., Chen, V., Garcia, D., Stojadinovic, O., Hower, S., Plano, G. V., Thaller, S. R., Tomic-Canic, M., & Strbo, N. (2020). Staphylococcus epidermidis Boosts Innate Immune Response by Activation of Gamma Delta T Cells and Induction of Perforin-2 in Human Skin. Frontiers in Immunology, 11.

Acharya Tankeshwar

Hello, thank you for visiting my blog. I am Tankeshwar Acharya. Blogging is my passion. As an asst. professor, I am teaching microbiology and immunology to medical and nursing students at PAHS, Nepal. I have been working as a microbiologist at Patan hospital for more than 10 years.

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