Metagenomic Studies in Inflammatory Skin Diseases

Godlewska, Urszula; Brzoza, Piotr; Kwiecień, Kamila; Kwitniewski, Mateusz; Cichy, Joanna

doi:10.1007/s00284-020-02163-4

Cited by 15 publications

(10 citation statements)

References 102 publications

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“…Thanks to the metagenomic approach, today, we are able to detect bacteria that cannot be cultivated. The term metagenomics refers to the use of modern genomic techniques for sequencing large sets of genes in a sample, without the need to isolate a particular species [ 9 ].…”

Section: Microbiota Analysis Methodsmentioning

confidence: 99%

“…Microbiome shifts in most common inflammatory skin diseases.Atopic dermatitis↑ Staphylococcus spp.1 3 7 8 ↑ Staphylococcus aureus 1 2 3 4 5 6 8 ↑ Staphylococcus epidermidis1 4 7 ↓ Streptococcus spp. 1 ↓ Cutibacterium spp.1 3 ↓ Corynebacterium spp.1 3 Psoriasis ↑ Firmicutes9 10 ↑ Proteobacteria11 14 ↑ Streptococcus spp 9. ↑ Prevotella 10 ↑ Staphylococcus spp 10.…”

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confidence: 99%

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Features of the Skin Microbiota in Common Inflammatory Skin Diseases

Ferček

Lugović-Mihić

Tambić-Andrašević

et al. 2021

Life

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Many relatively common chronic inflammatory skin diseases manifest on the face (seborrheic dermatitis, rosacea, acne, perioral/periorificial dermatitis, periocular dermatitis, etc.), thereby significantly impairing patient appearance and quality of life. Given the yet unexplained pathogenesis and numerous factors involved, these diseases often present therapeutic challenges. The term “microbiome” comprises the totality of microorganisms (microbiota), their genomes, and environmental factors in a particular environment. Changes in human skin microbiota composition and/or functionality are believed to trigger immune dysregulation, and consequently an inflammatory response, thereby playing a potentially significant role in the clinical manifestations and treatment of these diseases. Although cultivation methods have traditionally been used in studies of bacterial microbiome species, a large number of bacterial strains cannot be grown in the laboratory. Since standard culture-dependent methods detect fewer than 1% of all bacterial species, a metagenomic approach could be used to detect bacteria that cannot be cultivated. The skin microbiome exhibits spatial distribution associated with the microenvironment (sebaceous, moist, and dry areas). However, although disturbance of the skin microbiome can lead to a number of pathological conditions and diseases, it is still not clear whether skin diseases result from change in the microbiome or cause such a change. Thus far, the skin microbiome has been studied in atopic dermatitis, seborrheic dermatitis, psoriasis, acne, and rosacea. Studies on the possible association between changes in the microbiome and their association with skin diseases have improved the understanding of disease development, diagnostics, and therapeutics. The identification of the bacterial markers associated with particular inflammatory skin diseases would significantly accelerate the diagnostics and reduce treatment costs. Microbiota research and determination could facilitate the identification of potential causes of skin diseases that cannot be detected by simpler methods, thereby contributing to the design and development of more effective therapies.

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Section: Microbiota Analysis Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Features of the Skin Microbiota in Common Inflammatory Skin Diseases

Ferček

Lugović-Mihić

Tambić-Andrašević

et al. 2021

Life

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“…The sequence of the gene staphylococcal esxA was completely recovered in the data obtained from sample B. This gene is coding for the protein EsxA, a virulence factor present in S. aureus strains recovered from lesions of psoriatic patients but absent from strains found at unaffected sites [ 65 ].…”

Section: Resultsmentioning

confidence: 99%

First Description of the Composition and the Functional Capabilities of the Skin Microbial Community Accompanying Severe Scabies Infestation in Humans

et al. 2021

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Epidemiological studies link Sarcoptes scabiei infection and impetigo. Scabies mites can promote Streptococcus pyogenes (Group A Streptococcus) and Staphylococcus aureus infections by breaching the skin barrier and excreting molecules that inhibit host innate immune responses. However, little is known about the composition and the function of the scabies-associated microbiota. Here, high-throughput whole-metagenome sequencing was used to explore the scabies-associated microbiome. Scabies mites including their immediate microenvironments were isolated from two patients with severe scabies in Northern Australia. Two ~45–50 million paired-end reads Illumina libraries were generated of which ~2 (5.1%) and 0.7 million (1.3%) microbial reads were filtered out by mapping to human (hg19) and mite draft genomes. Taxonomic profiling revealed a microbial community dominated by the phylum Firmicutes (A: 79% and B: 59%) and genera that comprise Streptococcus, Staphylococcus, Acinetobacter, and Corynebacterium. Assembly of the metagenome reads resulted in genome bins representing reference genomes of Acinetobacter baumannii, Streptococcus dysgalactiae (Group C/G), Proteus mirablis and Staphylococcus aureus. The contigs contained genes relevant to pathogenicity and antibiotics resistance. Confocal microscopy of a patient skin sample confirmed A. baumannii, Streptococci and S. aureus in scabies mite gut and faeces and the surrounding skin. The study provides fundamental evidence for the association of opportunistic pathogens with scabies infection.

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“…Indeed, the research that has applied culture-independent approaches and NGS technology has produced the main advancements in our knowledge of the composition and function of this microbial community. Therefore, we mainly focused on such recent literature [ 17 , 18 , 19 , 20 , 21 , 22 ].…”

Section: References Analyzed and Methodologies Of Studymentioning

confidence: 99%

A Journey on the Skin Microbiome: Pitfalls and Opportunities

Pistone

Meroni

Panelli

et al. 2021

IJMS

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The human skin microbiota is essential for maintaining homeostasis and ensuring barrier functions. Over the years, the characterization of its composition and taxonomic diversity has reached outstanding goals, with more than 10 million bacterial genes collected and cataloged. Nevertheless, the study of the skin microbiota presents specific challenges that need to be addressed in study design. Benchmarking procedures and reproducible and robust analysis workflows for increasing comparability among studies are required. For various reasons and because of specific technical problems, these issues have been investigated in gut microbiota studies, but they have been largely overlooked for skin microbiota. After a short description of the skin microbiota, the review tackles methodological aspects and their pitfalls, covering NGS approaches and high throughput culture-based techniques. Recent insights into the “core” and “transient” types of skin microbiota and how the manipulation of these communities can prevent or combat skin diseases are also covered. Finally, this review includes an overview of the main dermatological diseases, the changes in the microbiota composition associated with them, and the recommended skin sampling procedures. The last section focuses on topical and oral probiotics to improve and maintain skin health, considering their possible applications for skin diseases.

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Metagenomic Studies in Inflammatory Skin Diseases

Cited by 15 publications

References 102 publications

Features of the Skin Microbiota in Common Inflammatory Skin Diseases

Features of the Skin Microbiota in Common Inflammatory Skin Diseases

First Description of the Composition and the Functional Capabilities of the Skin Microbial Community Accompanying Severe Scabies Infestation in Humans

A Journey on the Skin Microbiome: Pitfalls and Opportunities

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