Isolation and characterisation of bacteriophages from the human skin microbiome that infect Staphylococcus epidermidis

Abstract Phage therapy might be a useful approach for the treatment of nosocomial infections; however, only few lytic phages suitable for this application are available for the opportunistic pathogen, Staphylococcus epidermidis. In the current study, we developed an efficient method to isolate bacteriophages present within the human skin microbiome, by using niche-specific S. epidermidis as the host for phage propagation. S.epidermidis was identified on the forehead of 92% of human subjects tested. These isolates were then used to propagate phages present in the same skin sample. Plaques were observable on bacterial lawns in 46% of the cases where S. epidermidis was isolated. Eight phage genomes were genetically characterized, including the previously described phage 456. Six phage sequences were unique, and spanned each of the major staphylococcal phage families; Siphoviridae (n = 3), Podoviridae (n = 1), and Myoviridae (n = 2). One of the myoviruses (vB_SepM_BE06) was identified on the skin of three different humans. Comparative analysis identified novel genes including a putative N-acetylmuramoyl-L-alanine amidase gene. The host-range of each unique phage was characterized using a panel of diverse staphylococcal strains (n = 78). None of the newly isolated phages infected more than 52% of the S. epidermidis strains tested (n = 44), and non-S. epidermidis strains where rarely infected, highlighting the narrow host-range of the phages. One of the phages (vB_SepM_BE04) was capable of killing staphylococcal cells within biofilms formed on polyurethane catheters. Uncovering a richer diversity of available phages will likely improve our understanding of S. epidermidis-phage interactions, which will be important for future therapy.

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Staphylococcus epidermidis in the human skin microbiome mediates fermentation to inhibit the growth of Propionibacterium acnes: implications of probiotics in acne vulgaris

Applied Microbiology and Biotechnology ◽

10.1007/s00253-013-5394-8 ◽

2013 ◽

Vol 98 (1) ◽

pp. 411-424 ◽

Cited By ~ 86

Author(s):

Yanhan Wang ◽

Sherwin Kuo ◽

Muya Shu ◽

Jinghua Yu ◽

Stephen Huang ◽

...

Keyword(s):

Human Skin ◽

Staphylococcus Epidermidis ◽

Propionibacterium Acnes ◽

Acne Vulgaris ◽

Skin Microbiome

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Staphylococcus epidermidis: A Potential New Player in the Physiopathology of Acne?

Dermatology ◽

10.1159/000499858 ◽

2019 ◽

Vol 235 (4) ◽

pp. 287-294 ◽

Cited By ~ 13

Author(s):

Jean-Paul Claudel ◽

Nicole Auffret ◽

Marie-Thérèse Leccia ◽

Florence Poli ◽

Stéphane Corvec ◽

...

Keyword(s):

Human Skin ◽

Staphylococcus Epidermidis ◽

Skin Disease ◽

Potential Role ◽

Current Knowledge ◽

Treatment Options ◽

Skin Microbiome ◽

Cutibacterium Acnes ◽

Skin Commensals

Background: Cutibacterium acnes has been identified as one of the main triggers of acne. However, increasing knowledge of the human skin microbiome raises questions about the role of other skin commensals, such as Staphylococcus epidermidis, in the physiopathology of this skin disease. Summary: This review provides an overview of current knowledge of the potential role of S. epidermidis in the physiopathology of acne. Recent research indicates that acne might be the result of an unbalanced equilibrium between C. acnes and S. epidermidis,according to dedicated interactions. Current treatments act on C. acnesonly. Other treatment options may be considered, such as probiotics derived from S. epidermidis to restore the naturally balanced microbiota or through targeting the regulation of the host’s AMP mediators. Key Messages: Research seems to confirm the beneficial role of S. epidermidis in acne by limiting C. acnes over-colonisation and inflammation.

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5-methyl Furfural Reduces the Production of Malodors by Inhibiting Sodium l-lactate Fermentation of Staphylococcus epidermidis: Implication for Deodorants Targeting the Fermenting Skin Microbiome

Microorganisms ◽

10.3390/microorganisms7080239 ◽

2019 ◽

Vol 7 (8) ◽

pp. 239 ◽

Cited By ~ 3

Author(s):

Manish Kumar ◽

Binderiya Myagmardoloonjin ◽

Sunita Keshari ◽

Indira Putri Negari ◽

Chun-Ming Huang

Keyword(s):

Carbon Source ◽

Human Skin ◽

Negative Feedback ◽

Staphylococcus Epidermidis ◽

Fermentation Process ◽

Feedback Regulation ◽

Acetolactate Synthase ◽

Skin Microbiome ◽

Negative Feedback Regulation ◽

Lactate Fermentation

Staphylococcus epidermidis (S. epidermidis) is a common bacterial colonizer on the surface of human skin. Lactate is a natural constituent of skin. Here, we reveal that S. epidermidis used sodium l-lactate as a carbon source to undergo fermentation and yield malodors detected by gas colorimetric tubes. Several furan compounds such as furfural originating from the fermentation metabolites play a role in the negative feedback regulation of the fermentation process. The 5-methyl furfural (5MF), a furfural analog, was selected as an inhibitor of sodium l-lactate fermentation of S. epidermidis via inhibition of acetolactate synthase (ALS). S. epidermidis treated with 5MF lost its ability to produce malodors, demonstrating the feasibility of using 5MF as an ingredient in deodorants targeting malodor-causing bacteria in the skin microbiome.

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Complete Genome Sequences of Staphylococcus epidermidis Myophages Quidividi, Terranova, and Twillingate

Microbiology Resource Announcements ◽

10.1128/mra.00598-19 ◽

2019 ◽

Vol 8 (26) ◽

Cited By ~ 1

Author(s):

Miranda E. Freeman ◽

Sarah E. Kenny ◽

Amanda Lanier ◽

Katie Cater ◽

Mary C. Wilhite ◽

...

Keyword(s):

Human Skin ◽

Staphylococcus Epidermidis ◽

Complete Genome ◽

Opportunistic Pathogen ◽

Genome Sequences ◽

Gram Positive ◽

Content Type ◽

Mucous Membranes

Staphylococcus epidermidis is an opportunistic pathogen that commonly colonizes human skin and mucous membranes. We report here the complete genome sequences of three S. epidermidis phages, Quidividi, Terranova, and Twillingate, which are members of the Twort-like group of large myophages infecting Gram-positive hosts.

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SkinBug: an artificial intelligence approach to predict human skin microbiome-mediated metabolism of biotics and xenobiotics

iScience ◽

10.1016/j.isci.2020.101925 ◽

2021 ◽

Vol 24 (1) ◽

pp. 101925

Author(s):

Shubham K. Jaiswal ◽

Shitij Manojkumar Agarwal ◽

Parikshit Thodum ◽

Vineet K. Sharma

Keyword(s):

Artificial Intelligence ◽

Human Skin ◽

Skin Microbiome ◽

Intelligence Approach ◽

Artificial Intelligence Approach

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Complete Genome Sequence of Malassezia restricta CBS 7877, an Opportunist Pathogen Involved in Dandruff and Seborrheic Dermatitis

Microbiology Resource Announcements ◽

10.1128/mra.01543-18 ◽

2019 ◽

Vol 8 (6) ◽

Cited By ~ 4

Author(s):

Stanislas C. Morand ◽

Morgane Bertignac ◽

Agnes Iltis ◽

Iris C. R. M. Kolder ◽

Walter Pirovano ◽

...

Keyword(s):

Human Skin ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Seborrheic Dermatitis ◽

Skin Microbiome ◽

Basidiomycetous Yeasts ◽

Content Type ◽

Opportunist Pathogen ◽

Malassezia Restricta

Malassezia restricta, one of the predominant basidiomycetous yeasts present on human skin, is involved in scalp disorders. Here, we report the complete genome sequence of the lipophilic Malassezia restricta CBS 7877 strain, which will facilitate the study of the mechanisms underlying its commensal and pathogenic roles within the skin microbiome.

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Secretory Proteases of the Human Skin Microbiome

Infection and Immunity ◽

10.1128/iai.00397-21 ◽

2021 ◽

Author(s):

Wisely Chua ◽

Si En Poh ◽

Hao Li

Keyword(s):

Human Skin ◽

Hydrolytic Enzymes ◽

Microbial Interactions ◽

Skin Microbiome ◽

Protein Cleavage ◽

Wide Range ◽

Range Of Functions ◽

Diverse Community ◽

Secreted Proteases ◽

Pathogenic Agents

The human skin is our outermost layer and serves as a protective barrier against external insults. Advances in next generation sequencing have enabled the discoveries of a rich and diverse community of microbes - bacteria, fungi and viruses that are residents of this surface. The genomes of these microbes also revealed the presence of many secretory enzymes. In particular, proteases which are hydrolytic enzymes capable of protein cleavage and degradation are of special interest in the skin environment which is enriched in proteins and lipids. In this minireview, we will focus on the roles of these skin-relevant microbial secreted proteases, both in terms of their widely studied roles as pathogenic agents in tissue invasion and host immune inactivation, and their recently discovered roles in inter-microbial interactions and modulation of virulence factors. From these studies, it has become apparent that while microbial proteases are capable of a wide range of functions, their expression is tightly regulated and highly responsive to the environments the microbes are in. With the introduction of new biochemical and bioinformatics tools to study protease functions, it will be important to understand the roles played by skin microbial secretory proteases in cutaneous health, especially the less studied commensal microbes with an emphasis on contextual relevance.

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Impact of pH on growth of Staphylococcus epidermidis and Staphylococcus aureus in vitro

Journal of Medical Microbiology ◽

10.1099/jmm.0.001421 ◽

2021 ◽

Vol 70 (9) ◽

Author(s):

Vidula Iyer ◽

Janhavi Raut ◽

Anindya Dasgupta

Keyword(s):

Staphylococcus Aureus ◽

Growth Kinetics ◽

Staphylococcus Epidermidis ◽

Type Species ◽

Ph Dependence ◽

Skin Microbiome ◽

Content Type ◽

Link Type ◽

Kinetics Of

The pH of skin is critical for skin health and resilience and plays a key role in controlling the skin microbiome. It has been well reported that under dysbiotic conditions such as atopic dermatitis (AD), eczema, etc. there are significant aberrations of skin pH, along with a higher level of Staphylococcus aureus compared to the commensal Staphylococcus epidermidis on skin. To understand the effect of pH on the relative growth of S. epidermidis and S. aureus , we carried out simple in vitro growth kinetic studies of the individual microbes under varying pH conditions. We demonstrated that the growth kinetics of S. epidermidis is relatively insensitive to pH within the range of 5–7, while S. aureus shows a stronger pH dependence in that range. Gompertz’s model was used to fit the pH dependence of the growth kinetics of the two bacteria and showed that the equilibrium bacterial count of S. aureus was the more sensitive parameter. The switch in growth rate happens at a pH of 6.5–7. Our studies are in line with the general hypothesis that keeping the skin pH within an acidic range is advantageous in terms of keeping the skin microbiome in balance and maintaining healthy skin.

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