Oral Microbiology Lab

Our group is focused on molecular mechanisms governing oral biofilm formation, with a particular emphasis on selectively inhibiting pathogens while preserving commensal microorganisms. We investigate the potential of natural compounds with strong antibacterial and antibiofilm properties in preventing the proliferation of cariogenic bacteria and mitigating the virulence of dental biofilm.

Moreover, we explore the regulatory network of the nucleotide second messenger signalling in oral pathogens, orchestrating by c-di-AMP, c-di-GMP, and (p)ppGpp, to selectively modulate bacterial virulence and their interactions within the oral microbiome.

We are also dedicated to developing advanced biofilm models specifically tailored to study bacterial adhesion on dental surfaces, their interaction within complex microbial community and with the host tissues.

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Erdgeschoss

Notfall Erwachsene
Klinik für Oralchirurgie
Zentrum für Senioren­­zahn­medizin
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1. Obergeschoss

Notfall Kinder
Klinik für Kinder- & Jugend­­zahnmedizin
Klinik für Kiefer­orthopädie
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2. Obergeschoss

Behandlung Studierende
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3. Obergeschoss

Klinik für Allgemeine Zahnmedizin
Klinik für Oral Health & Medicine
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4. Obergeschoss

Klinik für Zahnerhaltung
Klinik für Rekonstruktive Zahnmedizin
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Our Team

Oral Microbiology Lab is actively involved in

  • Basic Research Projects – Investigating microbial ecology, biofilm dynamics, and antimicrobial agents.
  • Clinical Studies – Providing methodological support and scientific expertise to clinical research conducted by UZB clinicians, ensuring microbiological analysis and data interpretation.
  • Teaching & Training – Educating the next generation of scientists and clinicians in their Bachelor and Master curriculum in dentistry as well as during their postgraduate training. In addition, we welcome students from secondary schools (Gymnasium or Berufsschule) for a practical work experience (Schnuppertage) or to do their high school thesis (Maturaarbeit) in our labs.
  • Industry Collaboration – Partnering with biotech and pharmaceutical companies to develop innovative therapeutic solutions and oral care products.

Our Team

Monika Astasov-Frauenhoffer, PhD

PhD
Monika Astašov-Frauenhoffer

Co-group Leader Oral Microbiology,
Research Scientist

E-Mail
ORCID

Viktoriya Shyp, PhD

PhD
Viktoriya Shyp

Co-group Leader Oral Microbiology,
Research Scientist

E-Mail
ORCID

Eva M. Kulik, PhD

PhD
Eva M. Kulik

Senior Research Scientist,
Biosafety Officer,
Lab Manager

E-Mail
ORCID

 
Birte Bennecke

Administrative Assistant Research 

0041 61 267 26 00
E-Mail

MSc
Elisabeth Filipuzzi

Academic technical assistant

E-Mail

Dipl.-Ing.
Markus Steineck

Engineer, Deputy Lab Manager

E-Mail
ORCID

Biomedical Analyst HF
Hedwig Wariwoda

Technical assistant

E-Mail

BSc
Juliana Imholz

Lab technician

E-Mail

 
Layla Brachat

Intern

E-Mail

Med. dent.
Robert Borgos

Dr. med. dent. candidate

E-Mail

Med. dent.
Céline Chan

Dr. med. dent. candidate

E-Mail

Med. dent.
Julien Kneubühler

Dr. med. dent. candidate

E-Mail

Med. dent.
Pearly Perumpallil

Dr. med. dent. candidate

E-Mail

Med. dent.
Irina Poncioni

Dr. med. dent. candidate

E-Mail

Med. dent.
Lisa Stäuble

Dr. med. dent. candidate

E-Mail

Selected Projects, Grants and Collaborations

Bacterial adhesion

(all hard and soft surfaces in oral cavity)

Adhesion to oral surfaces

We develop in vitro models to investigate bacterial adhesion on different kind of materials found in the oral cavity, from enamel and implant surfaces to a 3D soft tissue model. These models enable comprehensive evaluation of surface modifications, antimicrobial properties, and tissue regeneration strategies.

We utilize a range of molecular and microbiological techniques – such as bacterial cultivation, biofilm formation assays under static and in flow conditions using both aerobic as well as anaerobic settings, fluorescence microscopy, PCR, ELISA, and calorimetric measurements – to assess how different material surfaces influence bacterial colonization and biofilm development.

By integrating these in vitro models with analytical methods our work contributes to the development of dental materials that not only resist bacterial adhesion but also possibly promotes tissue regeneration, thereby enhancing the longevity and success of dental restorations and implants for the patients in the future.

Publications
  • Monika Astasov-Frauenhoffer, PhD
    Monika Astasov-Frauenhoffer, PhD

2025

Ashrafi F, Astasov-Frauenhoffer M, Fasler-Kan E, Ruggiero S, Steiner R, Marot L, Sanchez F, Kühl S, Bornstein MM, Mukaddam K. Adhesion of Porphyromonas gingivalis and growth of human gingival fibroblasts on modified titanium dental implant surfaces exhibiting 1000-nm spikes. Quintessence Int. 2025 Feb 24;0(0):0. doi: 10.3290/j.qi.b5993849
https://www.quintessence-publishing.com/deu/en/article/5993849

2024

Astasov-Frauenhoffer M, Marot L, Sanchez F, Steiner R, Lohberger B, Bornstein MM, Wagner RS, Kühl S, Mukaddam K. Effects of nanomodified titanium surfaces considering bacterial colonization and viability of osteoblasts and fibroblasts. J Biomed Mater Res A. 2024 Dec;112(12):2160-2169. doi: 10.1002/jbm.a.37768.
https://onlinelibrary.wiley.com/doi/full/10.1002/jbm.a.37768

Karacic J, Ruf M, Herzog J, Astasov-Frauenhoffer M, Sahrmann P. Effect of Dentifrice Ingredients on Volume and Vitality of a Simulated Periodontal Multispecies Biofilm. Dent J (Basel). 2024 May 13;12(5):141. doi: 10.3390/dj12050141.
https://www.mdpi.com/2304-6767/12/5/141

2023

Meier D, Astasov-Frauenhoffer M, Waltimo T, Zaugg LK, Rohr N, Zitzmann NU. Biofilm formation on metal alloys and coatings, zirconia, and hydroxyapatite as implant materials in vivo. Clin Oral Implants Res. 2023 Oct;34(10):1118-1126. doi: 10.1111/clr.14146.
https://onlinelibrary.wiley.com/doi/full/10.1111/clr.14146

Mukaddam K, Astasov-Frauenhoffer M, Fasler-Kan E, Ruggiero S, Alhawasli F, Kisiel M, Meyer E, Köser J, Bornstein MM, Wagner RS, Kühl S. Piranha-etched titanium nanostructure reduces biofilm formation in vitro. Clin Oral Investig. 2023 Oct;27(10):6187-6197. doi: 10.1007/s00784-023-05235-4.
https://link.springer.com/article/10.1007/s00784-023-05235-4

Astasov-Frauenhoffer M, Göldi L, Rohr N , Worreth S, Dard E, Hünerfauth S, Töpper T, Zurflüh J, Braissant O. Antimicrobial and mechanical assessment of cellulose-based thermoformable material for invisible dental braces with natural essential oils protecting from biofilm formation. Sci Rep Aug 18;13(1). doi: 10.1038/s41598-023-39320-1
https://www.nature.com/articles/s41598-023-39320-1

Funding / Collaborators

Antibiofilm/Antibacterial Therapies

Our research focuses on developing innovative antibiofilm therapies to combat cariogenic and pathogenic biofilms associated with oral diseases such as dental caries and periodontitis. We explore a diverse range of strategies, including the use of natural antibiofilm compounds - such as plant-derived flavonoids - alongside probiotics and commercial antibacterial products.

These agents are tested for their ability to inhibit initial bacterial adhesion, disrupt mature biofilm structure, and modulate microbial community composition without promoting resistance. Using in vitro mono- and multispecies biofilm models, microfluidic devices, and high-resolution imaging, we assess the efficacy and mechanisms of action of these compounds under clinically relevant conditions.

Additionally, we evaluate their effects on host cells and the inflammatory response, aiming to identify approaches that support both microbial control and host tissue compatibility. This research contributes to the development of safer, resistance-free therapies that improve oral and systemic health outcomes through targeted oral biofilm modulation.

Publications
  • Monika Astasov-Frauenhoffer, PhD
    Monika Astasov-Frauenhoffer, PhD
  • Eva M. Kulik, PhD
    Eva M. Kulik, PhD
  • Viktoriya Shyp, PhD
    Viktoriya Shyp, PhD

2025

Rudin L, Kneubühler J, Dubey BN, Ahmad S, Bornstein MM, Shyp V. Inhibitory effect of plant flavonoid cyanidin on oral microbial biofilm. Microbiol Spectr. 2025 Jun 3;13(6):e0284824. doi: 10.1128/spectrum.02848-24
https://journals.asm.org/doi/10.1128/spectrum.02848-24

Seth-Smith HMB, Egli A, GautschS, Bornstein MM, Kulik EM. GenomicanalysisofLegionella pneumophilain thedrinkingwatersystemofa large buildingover25 years. MicrobGenom. 2025 May;11(5). doi: 10.1099/mgen.0.001393
https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001393

2024

Karacic J, Ruf M, Herzog J, Astasov-Frauenhoffer M, Sahrmann P. Effect of Dentifrice Ingredients on Volume and Vitality of a Simulated Periodontal Multispecies Biofilm. Dent J (Basel). 2024 May 13;12(5):141. doi: 10.3390/dj12050141.
https://www.mdpi.com/2304-6767/12/5/141

Reichardt E, Shyp V, Alig L, Verna C, Kulik EM, Bornstein MM. Antimicrobial effect of probiotic bacteriocins on Streptococcus mutans biofilm in a dynamic oral flow chamber model - an in vitro study. J Oral Microbiol. 2024 Jan 28;16(1):2304971. doi: 10.1080/20002297.2024.2304971
https://www.tandfonline.com/doi/full/10.1080/20002297.2024.2304971

2023

Tobler D, Braissant O, Waltimo T, Bornstein MM, Astasov-Frauenhoffer M. Stannous Source in Toothpastes Leads to Differences in Their Antimicrobial Efficacy. Oral Health Prev Dent. 2023 Sep 22;21:319-324. doi: 10.3290/j.ohpd.b4424911.
https://www.quintessence-publishing.com/deu/en/article/4424911

Astasov-Frauenhoffer M, Göldi L, Rohr N , Worreth S, Dard E, Hünerfauth S, Töpper T, Zurflüh J, Braissant O. Antimicrobial and mechanical assessment of cellulose-based thermoformable material for invisible dental braces with natural essential oils protecting from biofilm formation. Sci Rep Aug 18;13(1). doi: 10.1038/s41598-023-39320-1
https://www.nature.com/articles/s41598-023-39320-1

Rudin L, Roth N, Kneubühler J, Dubey BN, Bornstein MM, Shyp V. Inhibitory effect of natural flavone luteolin on Streptococcus mutans biofilm formation. Microbiol Spectr. 2023 Sep 21;11(5):e0522322. doi: 10.1128/spectrum.05223-22.
https://journals.asm.org/doi/10.1128/spectrum.05223-22

Rudin L, Bornstein MM, Shyp V. Inhibition of biofilm formation and virulence factors of cariogenic oral pathogen Streptococcus mutans by natural flavonoid phloretin. J Oral Microbiol. 2023 Jul 3;15(1):2230711. doi: 10.1080/20002297.2023.2230711
https://www.tandfonline.com/doi/full/10.1080/20002297.2023.2230711

Thurnheer T, Bensland S, Eick S, Kulik EM, Attin T, Karygianni L. Antibiotic Resistance among Fusobacterium, Capnocytophaga, and Leptotrichia Species of the Oral Cavity. Oral Health Prev Dent. 2023 Apr 4;21:93-102. doi: 10.3290/j.ohpd.b4009553.
https://www.quintessence-publishing.com/deu/en/article/4009553

Biofilm formation

(high sugar diet, poor hygiene, dysbiosis)

Antibiofilm therapies

(natural antibiofilm compounds, antibiofilm surfaces,
probiotics, antibacterial products)

Funding / Collaborators

cyclic-di-AMP   /   (p)ppGpp

Molecular mechanism of biofilm formation

Bacterial second messengers such as cyclic-di-AMP (c-di-AMP) and guanosine pentaphosphate or tetraphosphate ((p)ppGpp) are central regulators of bacterial physiology, biofilm formation, and stress responses within microbial communities. Our research aims to uncover how these nucleotide-based signaling molecules control virulence traits, interspecies communication, and adaptation in key oral pathogens including oral streptococci and periodontal pathogens.

By applying gene knockout strategies, transcriptomics and proteomics profiling, we aim to identify second messenger-dependent regulatory networks that influence biofilm formation, acid tolerance, antimicrobial resistance, and bacterial competitiveness within microbiome. Understanding these signaling systems could lead to novel therapeutic targets for selectively disrupting pathogenic biofilm behavior without harming beneficial members of the oral microbiome.

Publications
  • Viktoriya Shyp, PhD
    Viktoriya Shyp, PhD

2023

Dubey BN, Shyp V, Fucile G, Sondermann H, Jenal U, Schirmer T. Mutant structure of metabolic switch protein in complex with monomeric c-di-GMP reveals a potential mechanism of protein-mediated ligand dimerization. Sci Rep. 2023 Feb 21;13(1):2727. doi: 10.1038/s41598-023-29110-0.
https://www.nature.com/articles/s41598-023-29110-0

2021

Shyp V, Dubey BN, Böhm R, Hartl J, Nesper J, Vorholt JA, Hiller S, Schirmer T, Jenal U. Reciprocal growth control by competitive binding of nucleotide second messengers to a metabolic switch in Caulobacter crescentus. Nat Microbiol. 2021 Jan;6(1):59-72. doi: 10.1038/s41564-020-00809-4.
https://www.nature.com/articles/s41564-020-00809-4

Funding / Collaborators

Alumni / Students

Undergraduate Students

Lea Furrer – M Dent Med
Michèle Grossmann – M Dent Med
Thamilisai Kalaichcheliyan – M Dent Med
Asvina Kaneshan – M Dent Med
Fabienne Müller – M Dent Med
Hana Steiger – M Dent Med
Melanie Tanner – M Dent Med
Valérie Thomas – M Dent Med
Svenja Zheng – M Dent Med

Alumni

2025

Anna-Marie Petricevic – Intern

2024

Lucille Rudin – Dr. med. dent.
Lisa Stäuble – M Dent Med
Livia Göldi – M Dent Med
Cérline Chan – M Dent Med
Alain Schuler – M Dent Med

2023

Irina Poncioni – M Dent Med
Pearly Permpallil – M Dent Med
Noélle Roth – M Dent Med
Elif Dogan – M Dent Med
Sally Koegel – Dr. med. dent.
Raphael Schmid – Dr. med. dent.
Dominique Tobler – Dr. med. dent.

2022

Laura Villani – M Dent Med
Lena Pultrone – Dr. med. dent.
Jérome Donati – M Dent Med

2021

Gabriel Gasser – M Dent Med
Andreina Grieshaber – Dr. med. dent.
Julia Mülli – Dr. med. dent.
Elena Steiger – Dr. med. dent.
Josiana Steiger – Dr. med. dent.
Barbara Zeller – Dr. med. dent.

2020

Stephanie Suppiger – Dr. med. dent.
Simone Stöckli – Dr. med. dent.

Open Positions

We are always happy to accommodate curios and motivated students for their master thesis and support PhD candidates or postdocs in applying for their own funding with us.

Thus, if you have experience in microbiology, molecular biology, biofilm research or related topics, please apply via email by providing your CV and a short motivation letter / project interest (max 1 A4).