The Human Skin Microbiome in Selected Cutaneous Diseases

1The skin constitutes the external barrier between the human body and the environment. Considering the appendages, it has an estimated area of 25 m2. Regional variations in skin temperature, humidity, sebaceous gland density, and pH create different ecological niches where bacteria, fungi, viruses, archaea, and mites can thrive.

2The human skin microbiome comprises the microorganisms together with their genetic elements and environmental interactions. Actinobacteria (36-51%), Firmicutes (24-34%), Proteobacteria (11-16%), and Bacteroidetes (6-9%) are the four major bacterial phyla found on the skin. In moist sites, the most abundant bacteria are Staphylococcus (Firmicutes) and Corynebacterium (Actinobacteria). Oily sites harbor the least diverse population where Cutibacterium (Actinobacteria) species are the most common isolates. Dry areas of the skin show the greatest diversity with varied colonization of the four phyla (Figure 1).

3Fungal species include Malassezia spp., Cryptococcus spp., Rhodotorula spp., Aspergillus spp., and Epicoccum spp. Malassezia spp. are the most common, comprising around 80% of the whole fungal flora. Demodex spp. are tiny mites living in the pilosebaceous follicles. Viruses have been the less investigated elements of the skin microbiota, cutaneous β and γ human papillomaviruses are commonly found on the skin surface but are scarce contrasted to the phages of the bacterial flora inhabiting the skin.

4Microbiota colonization begins at birth and its composition is influenced by the route of delivery. Afterward, the composition is determined by several intrinsic (skin site, intra– and interpersonal variability, ethnicity, gender, and age) and extrinsic (lifestyle, hygiene routine, cosmetic use, antibiotics, geographical location, climate, and seasonality) factors.

5The skin microbiome has essential roles in the maintenance of skin homeostasis, the protection against invading pathogens, and the modulation of the immune system.

6Dysbiosis refers to the lack of balance among microbial communities within certain areas of the body that may lead to the onset or progression of diseases. Several skin diseases such as atopic and seborrheic dermatitis, acne, alopecia areata, psoriasis and acne may result from dysbiosis.

7Atopic dermatitis (AD) is a chronic inflammatory dermatosis that affects between 15–20% of children and 2–10% of adults. AD results from an intricate interaction between genetic susceptibility, barrier dysfunction, innate and adaptive immunity, and microbiome.

8S. aureus colonization is common in AD with percentages varying from lesional (70%) to non–lesional (39%) sites, S. aureus strains in AD patients differ from those isolated from asymptomatic carriers. However, some patients do not exhibit S. aureus overexpression, demonstrating the variability of AD.

9Fyhrquist et al showed an increased abundance of S. aureus with depletion of S. epidermidis and Corynebacterium spp. among AD patients when compared to healthy controls. Further, genome–based assays demonstrated a change in the microbiome of AD patients before an outbreak, with loss of the diversity of cutaneous commensals and a predominance of S. aureus, the diversity returns to baseline once the disease is controlled. Whether S. aureus triggers AD or thrives because of the disease remains to be elucidated.

10S. epidermidis, a commensal present on non–inflamed skin, appears to be S. aureus best antagonist. S. epidermidis is thought to maintain skin microbiome balance by integrating innate immune pathways that control the function of effector T cells and exerting an antimicrobial function through the production of IL–1α by dendritic cells and keratinocytes, therefore limiting the ability of pathogens to establish infections. Further, the JK16 strain inhibits S. aureus biofilm formation. On clinical grounds, Byrd et al. showed that the less severe flares of AD had higher counts of S. epidermidis whereas the more severe flares were associated with S. aureus.

11S. aureus exploits AD–associated skin barrier defects with diminished antimicrobial peptides (β defensins, LL–, and dermcidin) and the low acid environment to achieve its colonization. S. aureus–derived toxins and proteases further damage the skin barrier and induce adaptive and innate immune responses (Table 1).

12Malassezia spp. colonization increases with AD severity and has been detected in up to 90% of skin lesions. Its pathophysiological role may be due to the activation of pro–inflammatory cytokines and autoreactive cells that increase the expression of TLR2 and TLR4 through the secretion of immunogenic proteins.

13Antimicrobial agents eradicate S. aureus however, they also affect other members of the skin microbiome, disrupting the homeostasis between species and generating bacterial resistance.

14Biotherapy uses the “protective” effect of commensal agents against pathogens to improve dysbiosis in patients with AD. Staphylococcus hominis, S. lugdunensis and S. epidermidis produce several molecules capable of synergizing the innate antimicrobial response against S. aureus.

15The beneficial effect and exact mechanism of action of biotherapy are still under investigation. Murine studies and some clinical trials, in which commensal bacteria were applied topically, showed improvement in both AD models and disease severity scales. A randomized 1–week trial of topical S. hominis A9 (ShA9) – isolated from healthy human skin – or vehicle on the forearm skin of 54 adults with S. aureus positive AD, met the primary endpoint of safety and resulted in a reduction of S. aureus colony unit formation in both lesional and non–lesional skin during treatment and up to 96 hours after discontinuation. Further, a double–blind, vehicle–controlled randomized clinical trial evaluated in 11 adult patients with moderate/severe AD if the autologous topical application of antimicrobial–producing coagulase negative Staphylococcus (CoNS) obtained from non–lesional skin of AD patients could inhibit S. aureus and improve clinical outcomes. S. aureus colonization was reduced (by 99.2%) and EASI scores improved in patients thar received active treatment compared with vehicle.

16Other therapies directed to the dysbiosis include narrow–band UVB phototherapy – which decreases the number of S. aureus and its production of superantigens – and the development of vaccines against S. aureus.

17Regarding the intestinal microbiome, a low diversity within the first weeks of life confers a higher risk of developing AD. Comparative studies of intestinal microbiome between patients with AD and healthy controls have revealed that Faeclibacerium prausnitzii and Ruminocococus gnavus are increased in patients with AD, whereas Bacteroides fragilis and Streptococcus salivaris, are less abundant. Therefore, those interventions that increase microbial diversity using prebiotics, probiotics, or symbiotics could prevent AD from developing in high–risk children.

18Seborrheic dermatitis (SD) is a common chronic inflammatory skin disease in both pediatric and adult ages, ranging from slight scalp scaling to severe erythematous plaques of the scalp, face, and trunk.

19The direct correlation of the number of yeasts with the severity of the disease and the symptomatic improvement of the affected skin after the use of antifungals support Malassezia’s relevant role in the pathogenesis of SD, however, some studies disagree with the findings. Thus, Malassezia’s overgrowth might be important only in predisposed individuals due to differences in sebaceous gland function, immune function, and lipid composition.

20Malassezia preferentially colonizes seborrheic areas of the skin, where it uses saturated fatty acids and disregards unsaturated fatty acids (oleic acid), that disrupt the barrier function and condition an inflammatory response in the skin.

21The interaction of Malassezia with epidermal cells, in susceptible individuals, stimulates antigen–presenting cells through pattern recognition receptors – TLR–, NOD–like, and C–type lectin receptors –, that activate several cell–signaling pathways such as MPAK, NF–κB, and NFAT leading to inflammation and secretion of pro–inflammatory cytokines and mediators. The inflammation further increases barrier dysfunction and dysbiosis.

22Sebaceous areas are also colonized by several bacteria whose role has been recently studied. Paulino et al. compared the bacterial and fungal microbiota of lesional and non–lesional skin in healthy controls and SD patients, finding greater diversity and variation in both bacteria and fungi in SD patients. Besides, Tanaka et al. studied the bacterial microbiota in lesional and non–lesional sites of 24 patients with SD, finding a predominance of Acinetobacter, Staphylococcus, and Streptococcus in lesional skin, whereas Cutibacterium predominated in non–lesional skin, and colonization by Corynebacterium was similar in both. Higher colonization rates of S. epidermidis have been found in facial seborrheic dermatitis in Chinese patients, and in HIV positive and negative patients with SD. One more recent report has mentioned that S. aureus is the most common bacterial member of the skin flora in patients with SD.

23Several studies have shown an increase in the Malassezia restricta/Malassezia globosa ratio and a reduction in the Cutibaterium/Staphylococcus ratio in SD. Staphyloccus is linked with epidermal barrier damage, including increased transepidermal water losses and pH, while Cutibacterium increases water content. Malassezia has also been associated with increased pruritus and disease severity.

24Some studies have focused on the use of probiotics to treat SD. Guéniche et al. showed a decrease in erythema, pruritus, and scaling with the topical application of Vitreoscilla filiformis in 60 patients. Besides, the oral administration of Lactobacillus paracasei improved erythema, seborrhea, and dandruff in patients with SD. The therapeutic effect may be related to a rise in the activity of regulatory T cells, and the secretion of IL–10 and transforming growth factor–beta by dendritic cells.

25Alopecia areata (AA) is a nonscarring type of hair loss with an incidence of 2% and a greater prevalence among pediatric populations. Hair loss can range from well–defined patches to diffuse or total hair loss, which can affect all hair–bearing sites.

26The pathogenesis of AA remains incompletely understood. It is believed that autoimmune–mediated HF destruction, the upregulation of inflammatory pathways, and loss of immune privilege in the hair follicle (HF) result in AA. Genetic predisposition, environmental factors, and recently the skin and gut microbiome have been related to autoimmunity in AA.

27The HF microbiota is located near the bulge (stem cell niche) and the bulb (cellular division site to build a new hear) considered immune–privileged sites. Shifts in the HF microbiome can be related to loss of homeostasis, modulation of immune reactions and the intense peribulbar inflammation in AA.

28Symbiosis of Corynebateriaceae, Propionibacteriaceae, Staphylococcaceae, and Malassezia is related to a healthy scalp, while dysbiosis can cause pathological conditions. Pinto et al. found microbial shifts in individuals with AA exhibiting over–colonization with C. acnes along with a reduced S. epidermidis abundance, however, it has not been determined if these differences are cause or consequence of the disease. The role of CMV in triggering AA was suggested after finding DNA sequences in biopsies of AA, but subsequent studies did not confirm this fact. Rudnicka et al. postulated a possible relation between scalp colonization by Alternaria spp. and AA after it was cultured from epidermal scrapings in patients.

29Along with skin, gut dysbiosis has been recently linked with AA. Genes that are related to AA can affect gut colonization with microorganisms that induce a Th1 response with increased IFNγ production. There are two cases of AA with long–term hair regrowth after fecal microbiota transplants that support a role of the intestinal microbiome in the pathophysiology of AA. Nonetheless, certain gut microbiota differences identified in patients with AA were not significant.

30AA is associated with other autoimmune disorders. Gut dysbiosis can act as a common pathway in patients with both inflammatory bowel disease and AA. A variety of factors involved in hair growth and/or maintaining immunological homeostasis are affected in gut dysbiosis: bacterial production of biotin, short–chain fatty acids produced by gut microbiota, vitamin D deficiency, among others. Restoration of gut microbiota balance might contribute to hair regrowth in patients with alopecia areata by enhancing the absorption and synthesis of nutrients and host–related factors such as immunomodulation.

31An innovative treatment option for AA is the therapeutic manipulation of the microbiome. This manipulation may be achieved by fecal microbiota transplant or the use of microbial metabolites such as postbiotics.

32Psoriasis vulgaris (PV) is a chronic inflammatory disorder with a worldwide prevalence of 2%. PV results from a complex interaction between genetic predisposition and environmental factors that incite immune dysregulation and trigger a rapid proliferation of keratinocytes and infiltration of immune cells with the formation of erythematous and scaly plaques.

33The breakdown of immune tolerance to cutaneous microorganisms has been implicated in the pathogenesis of PV. Bacteria found on PV plaques include Firmicutes, Actinobacteria, and Proteobacteria. Other authors have shown a decrease in Actinobacteria and Bacteroides and an increase in Coprobacillus, Ruminococcus, and Streptococcus.

34Several studies have shown increased numbers of Staphylococcus in both non–lesional (S. sciuri and S. aureus) and lesional skin (S. aureus and S. ptettenkoferi) when compared to the skin of healthy individuals. Whereas S. epidermidis, C. acnes and C. granulosum are more numerous in healthy than in psoriatic skin.

35S. aureus colonizes psoriatic lesions in 60% of the patients and up to 60% secrete enterotoxins and toxic shock syndrome toxin–1. Colonization by S. aureus is thought to trigger an inflammatory Th17 response responsible for the perpetuation of keratinocyte proliferation.

36S. pyogenes is also frequently identified as trigger for both the development and the exacerbations of PV. Pharyngeal infection by S. pyogenes induces superantigen activation of T cells. Th1 cells recognize group A Streptoccocus wall antigens and produce IFNγ, which is elevated in up to 70% of patients with guttate and chronic plaque psoriasis lesions. Additionally, superantigens located in the dermal layers bind directly to HLA–DR receptors on dendritic cells, macrophages, and keratinocytes, perpetuating inflammation.

37The association of Malassezia with PV is unclear. Its alleged involvement relies on Malassezia’s ability to invade keratinocytes which in turn increase the expression of TGFβ, integrin chains. and heat shock protein 70 that induce hyperproliferation. Besides, by the secretion of chemotactic factors, Malassezia attracts neutrophils to PV lesions.

38Candida albicans has been linked to skin lesion persistence and worsening, notably in inverse psoriasis. The mechanism remains unknown, however, it may be mediated by superantigens.

39Regarding viruses, patients infected by human immunodeficiency virus or human papillomavirus, have more severe features of psoriasis related to the secretion of substance P that stimulates the proliferation of keratinocytes.

40Several studies suggest that the intestine is the possible origin of the dysbiosis observed in psoriasis. The most frequently reported findings are the reduction of Bacteroides, and Akkermansia spp. and the increase of Firmicutes and Actinobacteria.

41The altered intestine leads to bacterial translocation, triggering inflammation and an aberrant microbiome, which produces a perpetuation of the inflammatory response. Inflammatory bowel disease and psoriasis have an association, the presence of Crohn’s disease increases up to 5 times the risk of developing psoriasis. In these patients, Faecalibacterium praunitziiis is reduced, limiting its anti–inflammatory effect through the inhibition of the NFκB pathway.

42The use of antibiotics to attack dysbiosis has shown improvement of psoriasis but with the cost of eradicating beneficial communities both in the intestine and on the skin.

43Probiotics have an immunomodulatory effect by increasing the production of immunoglobulins or activating lymphocytes and mononuclear cells. Navarro–López observed among 90 patients with psoriasis that the group of 45 patients that received mixed probiotics (Bifidobacterium longum, B. lactis, and Lactobacillus rhammosus) had a decrease in the severity of psoriasis, a better response rate to treatment, less need for steroids, and a lower risk of relapse.

44The use of prebiotics and symbiotics may have a beneficial effect as adjunctive treatments in psoriasis by modifying the inflammatory responses of CD4 + and CD8 + T lymphocytes. The role of fecal microbiota transplantation is under investigation to modify the intestinal microbiota and serve as therapy in psoriasis and its comorbidities.

45Acne is a chronic inflammatory disorder of the pilosebaceous follicle affecting more than 85% of adolescents and young adults. Its pathogenesis includes increased sebum production, follicular hyperkeratinization, skin microbiome, and Cutibacterium acnes, and inflammation.

46Acne has been largely associated with C. acnes proliferation. However, several authors have found that the abundance and bacterial load of C. acnes do not differ significantly between acne and healthy patients. Thus, it appears that the loss of the diversity between the six phylogenetic groups (IA1, IA2, IB, IC, II, and III) with predominance of IA1 and to a lesser degree IA2, rather than C. acnes proliferation plays a role in the triggering of acne.

47C. acnes triggers the release of proinflammatory cytokines after binding to TLR–2 that activate NLRP3 inflammasomes and caspase1–, driving the secretion of IL–1β, T cell differentiation and lymphocyte and neutrophil recruitment to acne lesions. TLR–2 activation also stimulates IL–1α production with a pivotal role in comedogenesis through the stimulation of keratinocyte proliferation. C. acnes can also form biofilms that increase virulence and resistance to antimicrobial treatments.

48S.epidermidis inhibits C. acnes proliferation by favoring the fermentation of glycerol and releasing succinic acid. It also reduces C. acnes–induced skin inflammation by the production of lipoteichoic acid which inhibits TLR2 production, and IL–6 and TNFα by keratinocytes. On the other hand, C. acnes inhibits S. epidermidis proliferation by keeping the acidic environment of the pilosebaceous follicle, hydrolyzing sebum triglycerides, and secreting propionic acid. The loss of balance between them induces the activation of inflammation–related markers (IL1ra, IL–, IL–, G–CSF) and other molecules (C5/C5a, soluble CD14 MIP–3beta, Serpin E, VCAM–, and β−defensin 2).

49Malassezia can also play a role in refractory acne. Its lipase, 100 times more active than that of C. acnes, attracts neutrophils and stimulates the release of pro–inflammatory cytokines from monocytes and keratinocytes. Its exact involvement in the pathogenesis of acne, however, has yet to be determined.

50Tetracyclines are frequently the first choice of treatment for moderate/severe acne since they suppress C. acnes growth and control of inflammation. However, the antimicrobial activity also modifies cutaneous microbiota that may be beneficial.

51Currently, the development of a vaccine against CAMP virulence factor to induce immunity has resulted – in ex vivo models – in decreased growth of C. acnes and proinflammatory toxins.

52Intermittent pulsed light improves the severity of acne, regulates the balance between S. epidermidis and C. acnes and inhibits sebum secretion. Recently, Yang et al. demonstrated, on 5 patients with moderate to severe acne, that photodynamic therapy increased the diversity of skin microbiome in acne and shifted follicular microbiome towards epidermal microbiome, exerting its beneficial effect partly by inhibiting C. acnes and modifying the composition and potential function of skin microbiome in acne.

53Molecular approaches to define microbial diversity have modified our understanding of the skin microbiome and raised several questions regarding the host–microbe interaction and its relevance to skin disease. Current knowledge has shown that bacterial, fungal, and viral species are under or overexpressed in several dermatoses when compared with healthy skin. To date, the pathogenic role of several species has been suggested in diverse skin diseases, such as C.acnes in acne or S. aureus in AD. However, the paradigm of the microbiome related to some skin diseases has shifted from the proliferation of one or more microorganisms to the loss of diversity among several microorganisms in producing disease.

54Despite the progress in identifying the variations of the skin microbiome, it is yet unclear if shifts in the microbiome play a causative role in the skin diseases here discussed or merely represent a consequence of the inflammatory microenvironment. Thus, more research is needed to fully understand how microbiome variations relate to the genetic and environmental factors that also contribute to the disease. Further analysis of microorganism interaction with the immune system and among each other, the relationship between the skin microbiome and other niches (such as the gut), and the modification on the growth conditions of microorganisms according with the host’s own intrinsic and extrinsic factors is still needed.

55As we gain a better knowledge of the skin microbiota, several unanswered questions will guide future research efforts directed towards understanding the intricate interactions controlling the host–microorganism relation and the possibility of the host and the microorganism developing together.

56Finally, as antimicrobial treatments directed against the pathogens associated with skin diseases also eradicate beneficial flora, investigation efforts have shifted to the maintenance of skin microbiota homeostasis through the utilization of probiotics, prebiotics, symbiotics, and fecal transplantation. In the close future, their real therapeutic effectiveness will certainly be established.

57SC–C made substantial contributions on the acquisition of data for the work, revised it critically for important intellectual content, provided approval for publication of the content and agrees to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. LO–C made substantial contributions to the design of the work, revised it critically for important intellectual content, provided approval for publication of the content, and agreed to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. MS–d–O made substantial contributions to the conception of the work, drafted the work, provided approval for publication of the content, and agreed to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

58This work was supported by the E022 Program from the Instituto Nacional de Pediatría.

59The authors declare that the research was conducted in the absence of any commercial or financial relationship that could be construed as a potential conflict.

60All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.