Three-Dimensional (3D) Microbiome and Infection Models

We develop 3D microbiome and infection skin models with an integrated immune system that can be used to study host-pathogen/microbiome interactions.

We use our reconstituted epidermis and full-thickness skin models made from specifically immortalized primary or primary cells as well as models supplemented with immune cells. The developed horny layer (stratum corneum) of the models is colonized with specific skin microbiome or pathogenic microorganisms according to the desired application. 

 

Microbiome skin models

are reconstructed models whose stratum corneum is colonized with commensal skin microbiome strains such as Staphylococcus ssp, e.g. S. epidermidis, or Micrococcus luteus [1, 2, 3].

 

Infection skin models

are reconstructed models whose stratum corneum is infected with pathogenic, opportunistic microorganisms such as Staphylococcus aureus, Staphylococcus pyogenes, Escherichia coli, Klebsiella ssp., Pseudomonas aeruginosa, Cutibacterium acnes, Herpes simplex virus 1, Candida albicans or Malassezia furfur, which can cause dermatological infections [4, 5]. 

Infektionshautmodell
© Fraunhofer IGB
Infektionshautmodell: A) Histologischer Schnitt eines humanen 3D-Vollhautmodells, dessen Stratum corneum mit C. albicans infiziert wurde. Bei der Invasion bis in die Dermis erfolgte eine für C. albicans typische morphogenetischen Veränderungen zu einer verlängerten Hyphenformen. B) Histologischer Schnitt eines humanen 3D-Vollhautmodells ergänzt um Immunzellen, dessen Stratum corneum mit C. albicans besiedelt wurde. Die Infektion mit C. albicans ist bis auf das Stratum corneum zurückgedrängt (erstellt mit Biorender.com).

Challenge: skin microbiome as part of the skin's natural protective function

The skin microbiome consists of different microorganisms and is part of the skin's natural protective mechanism. The main components are commensal microorganisms, which live closely with the host on the skin but do not harm it. 

Commensals can reduce the colonization of pathogenic bacteria on the skin cells. They can also strengthen the immune response to pathogenic bacteria by stimulating the production of interferon and other cytokines as well as phagocytosis [6].

 

Disruption of the microbiome balance through medication or cosmetics

However, the skin microbiome can also consist of pathogenic, opportunistic microorganisms that trigger diseases. In a healthy host, there is an individual balance between commensal and opportunistic microorganisms. This balance can shift in favor of opportunistic microorganisms due to weakened host defenses, altered hormone production, but also due to the use of drugs, cosmetics or personal care products. According to various studies, such changes in the skin microbiome are involved in the pathophysiology of various dermatoses [7].

 

Species-specific differences require specific skin models

Although many mouse models are used to study skin physiology and biology, mouse skin differs significantly from human skin in anatomical structure, gene expression, cytokine profile, antimicrobial peptides and the composition of proteins related to the skin barrier and forming the epidermal differentiation complex [8]. As a consequence, these species-specific differences in innate cutaneous defenses influence the interaction between skin and microbiota in different ways. It is therefore obvious that mouse skin is not a suitable model for studying the interaction between skin and the human microbiota and that mouse experiments with organisms of the human skin microbiome can lead to misleading conclusions [9]. 

Human 3D skin models with their fully differentiated epidermal barrier have been established as a valuable tool in dermatological research and are of major importance here [10]. 

Our development: human and animal 3D microbiome and infection models to study host reactions of the skin

With our decades of experience in cell line development, working with (pathogenic) microorganisms and adherence to the highest quality standards, we establish human and animal 3D microbiome and infectious skin models.

The skin models for investigating host reactions of the skin in the presence of microbiome or pathogenic microorganisms can contain immune cells in addition to components of the skin and the microorganisms. 

Schematische Darstellung der 3D-Hautmodelle unterschiedlicher Komplexität als immunkompetenten Mikrobiom- und Infektionsmodelle sowie als immunkompetente Mikrobiom- und Infektionsmodelle.
© Fraunhofer IGB
Schematische Darstellung der 3D-Hautmodelle unterschiedlicher Komplexität als immunkompetenten Mikrobiom- und Infektionsmodelle sowie als immunkompetente Mikrobiom- und Infektionsmodelle (erstellt mit BioRender.com).

Unique selling point: species-specific models with high validity

Our 3D microbiome and infection skin models are produced from specifically immortalized primary skin cells from healthy human or animal donors, such as dogs. These cells retain their physiological behavior and are also available indefinitely. 

Our species-specific 3D microbiome and infection models offer a variety of advantages [11]

  • Independence from donors,
  • High reproducibility,
  • A fully differentiated epidermis,
  • A simple simulation of inflammation or disease by adding cytokines or growth factors or by using targeted genetically modified skin cells that intrinsically increase inflammation and
  • Species-specific results and findings 

Application areas

Our 3D microbiome and infection skin models can be customized for specific applications and questions and are generally suitable for studying the effects of commensal microorganisms and skin pathogens in their natural host environment under physiological conditions. 

Our models are used for the

  • Assessment of the effects of cosmetic and dermatological products as well as pharmaceuticals and personal care products on the development of commensal microorganisms of the skin microbiome,
  • Development and testing of probiotic skin care products
  • Development and preclinical testing of antimicrobial agents to combat pathogenic microorganisms,
  • Analysis of the effects of bioactive textiles on skin microbiomes and pathogenic microorganisms and
  • Analysis of interactions between microorganisms and the skin or skin reactions to microorganisms 

Infection of reconstituted skin with a clinical isolate of C. albicans or a non-virulent strain.
© Fraunhofer IGB
Infection of reconstituted skin (A) with a clinical isolate (B), or an avirulent mutant (C). The clinical isolate penetrates the protective layer of keratinocytes and invades through the epithelial cell layers into the matrix, leading to disintegration of the model system after 48h (B). The avirulent mutant do not form hyphae and show no ability to invade into the tissue. These Candida cells are detected on the tissue surface only.

Range of services

We offer a wide range of services related to our skin models, which we carry out in state-of-the-art laboratories on behalf of and in collaboration with customers:

  • Carrying out efficacy studies
  • Development of innovative and complex 3D microbiome and infection skin models
  • Provision of skin models for shipping

Analysis methods

The analyses of 3D microbiome and infectious skin models can be performed with the full-thickness skin model as well as separately in dermis and epidermis and – if applicable – an underlying population of immune cells. 

Our analysis options include, among other things

  • Histological and immunohistochemical staining of tissue thin sections,
  • Microbiological analyses (vitality, quantification of colony-forming units)
  • Multiplex analyses for the determination of cytokine profiles and antimicrobial peptides
  • RNA and DNA analyses

Equipment

  • Molecular biology and microbiology laboratories for work according to safety levels L2, S1 and S2 GenTSV

Publications

  • Kühbacher A, Burger-Kentischer A, Rupp S. Interaction of Candida Species with the Skin. Microorganisms. 2017 Jun 7;5(2):32. doi: 10.3390/microorganisms5020032. PMID: 28590443; PMCID: PMC5488103.
  • Hiller E, Zavrel M, Hauser N, Sohn K, Burger-Kentischer A, Lemuth K, Rupp S. Adaptation, adhesion and invasion during interaction of Candida albicans with the host--focus on the function of cell wall proteins. Int J Med Microbiol. 2011 Jun;301(5):384-9. doi: 10.1016/j.ijmm.2011.04.004. Epub 2011 May 14. PMID: 21571590.
  • Kühbacher A, Sohn K, Burger-Kentischer A, Rupp S. Immune Cell-Supplemented Human Skin Model for Studying Fungal Infections. Methods Mol Biol. 2017;1508:439-449. doi: 10.1007/978-1-4939-6515-1_25. PMID: 27837520.
  • Hogk I, Rupp S, Burger-Kentischer A. 3D-tissue model for herpes simplex virus-1 infections. Methods Mol Biol. 2013;1064:239-51. doi: 10.1007/978-1-62703-601-6_17. PMID: 23996262.
  • Kühbacher A, Henkel H, Stevens P, Grumaz C, Finkelmeier D, Burger-Kentischer A, Sohn K, Rupp S. Central Role for Dermal Fibroblasts in Skin Model Protection against Candida albicans. J Infect Dis. 2017 Jun 1;215(11):1742-1752. doi: 10.1093/infdis/jix153. PMID: 28368492 
  • Jbara-Agbaria D, Blondzik S, Burger-Kentischer A, Agbaria M, Nordling-David MM, Giterman A, Aizik G, Rupp S, Golomb G. Liposomal siRNA Formulations for the Treatment of Herpes Simplex Virus-1: In Vitro Characterization of Physicochemical Properties and Activity, and In Vivo Biodistribution and Toxicity Studies. Pharmaceutics. 2022 Mar 13;14(3):633. doi: 10.3390/pharmaceutics14030633. PMID: 35336008 
  • Hogk I, Kaufmann M, Finkelmeier D, Rupp S, Burger-Kentischer A. An In Vitro HSV-1 Reactivation Model Containing Quiescently Infected PC12 Cells. Biores Open Access. 2013 Aug;2(4):250-7. doi: 10.1089/biores.2013.0019. PMID: 23914331; PMCID: PMC3731678.
  • Ron-Doitch S, Sawodny B, Kühbacher A, David MMN, Samanta A, Phopase J, Burger-Kentischer A, Griffith M, Golomb G, Rupp S. Reduced cytotoxicity and enhanced bioactivity of cationic antimicrobial peptides liposomes in cell cultures and 3D epidermis model against HSV. J Control Release. 2016 May 10;229:163-171. doi: 10.1016/j.jconrel.2016.03.025. Epub 2016 Mar 21. PMID: 27012977.

References

[1] Byrd, A., Belkaid, Y. & Segre, J. The human skin microbiome. Nat Rev Microbiol 16, 143–155 (2018). https://doi.org/10.1038/nrmicro.2017.157

[2] Grice, E., Segre, J. The skin microbiome. Nat Rev Microbiol 9, 244–253 (2011). https://doi.org/10.1038/nrmicro2537

[3] Carmona-Cruz S, Orozco-Covarrubias L and Sáez-de-Ocariz M (2022) The Human Skin Microbiome in Selected Cutaneous Diseases. Front. Cell. Infect. Microbiol. 12:834135. doi: 10.3389/fcimb.2022.834135

[4] Findley K, Grice EA (2014) The Skin Microbiome: A Focus on Pathogens and Their Association with Skin Disease. PLoS Pathog 10(11): e1004436. https://doi.org/10.1371/journal.ppat.1004436

[5] Byrd, A., Belkaid, Y. & Segre, J. The human skin microbiome. Nat Rev Microbiol 16, 143–155 (2018). https://doi.org/10.1038/nrmicro.2017.157

[6] Corey P. Parlet, Morgan M. Brown, Alexander R. Horswill, Commensal Staphylococci Influence Staphylococcus aureus Skin Colonization and Disease, Trends in Microbiology 27(6), 2019: 497-507, https://doi.org/10.1016/j.tim.2019.01.008

[7] Carmona-Cruz S, Orozco-Covarrubias L and Sáez-de-Ocariz M (2022) The Human Skin Microbiome in Selected Cutaneous Diseases. Front. Cell. Infect. Microbiol. 12:834135. doi: 10.3389/fcimb.2022.834135

[8] Emmert H, Rademacher F, Gläser R, Harder J. Skin microbiota analysis in human 3D skin models—“Free your mice”. Exp Dermatol. 2020; 29: 1133–1139. https://doi.org/10.1111/exd.14164

[9] Emmert H, Rademacher F, Gläser R, Harder J. Skin microbiota analysis in human 3D skin models—“Free your mice”. Exp Dermatol. 2020; 29: 1133–1139. https://doi.org/10.1111/exd.14164

[10] Rademacher F, Simanski M, Gläser R, Harder J. Skin microbiota and human 3D skin models. Exp Dermatol. 2018; 27: 489–494. https://doi.org/10.1111/exd.13517

[11] Rademacher F, Simanski M, Gläser R, Harder J. Skin microbiota and human 3D skin models. Exp Dermatol. 2018; 27: 489–494. https://doi.org/10.1111/exd.13517

 

Reference projects

December 2019 – November 2025

imSAVAR –

Immune Safety Avatar: Nonclinical mimicking of the immune system effects of immunomodulatory therapies

 

In the imSAVAR project, an interdisciplinary EU consortium is developing innovative model systems to identify side effects of immunomodulating therapeutics on the immune system and to develop new biomarkers for diagnosis and prognosis. Fraunhofer IGB is involved in the development of novel immunocompetent in vitro models based on organ‑on‑chip systems as well as of cell‑based reporter gene assays using receptors of the immune system. Furthermore, they are part of the project management team.

April 2017 – March 2020

InnateFun – stimulating antifungal innate immunity to combat fungal infections

 

Fungal infections are difficult to diagnose and treat and can lead to serious complications in hospitals. In the InnateFun project funded by the BMBF, Fraunhofer IGB is investigating whether immunomodulators – a virtually new type of antifungal agent – can stimulate the innate immune system in such a way that fungal infections can be combated efficiently.

October 2013 – September 2017

ImResFun – Identification of protective mechanisms of the skin using immunological 3D tissue models

 

In infection research in-vitro models are well suited for studying initial processes in the colonization of epithelial surfaces by pathogens. The aim of the network ImResFun is to find new means for fighting Candida infections.