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Skander Hathroubi

Ph.D in veterinary science, microbiologist and biofilm researcher

Biofilms: bacterial architectures
Bacterial cellulose active matters
Microbiology and Pathogenesis
  • Investigating E. coli macrocolony biofilms and their architectures. Role of cellulose and Curli. Interdisciplinary project (Cluster Matters of Activity)
    Joining the laboratory of Prof. Regine Hengge
  • Biofilm from architectural and design view
  • Textile fermentation_Biofilm
  • Exhibition at the Humboldt Labor at Humboldt Forum_2021 “After Nature”, “Active Curtain”, “La récolte des biofilms”
  • Book contribution:
    B. Beyer and S. Hathroubi. La récolte des biofilms. In: MàJ : design, environnements techniques & pratiques exploratoires. Éditions Cité du design. École supérieure d’art et design Saint-Étienne (ESADSE)/Cité du design, France. 2021
  • Investigating Helicobacter pylori biofilm formation and its potential role in pathogenesis in the lab of Dr. Karen Ottemann. Transcriptomic and genetic approaches to identify genes associated with H. pylori biofilm growth. Mouse-models for H. pylori infections and imaging approaches (CSLM and SEM) to characterize the biofilm structure its components.

    1. S. Hathroubi, S. Hu and K. M Ottemann. Genetic requirement and transcriptomics of Helicobacter pylori biofilm formation on abiotic and biotic surfaces. npj Biofilms Microbiomes 6, 56 (2020)
    2. S. Hathroubi, J. Zerebinski, A. Clark and K. M Ottemann. Helicobacter pylori biofilm confers antibiotic tolerance in part via a protein-dependent mechanism, Antibiotics 9(6):355. (2020)
    3. S. Hathroubi, S. L. Servetas, I. Windham, D. S. Merrell, K. M Ottemann. Helicobacter pylori biofilm formation and its potential role in pathogenesis. Microbiol and Mol Biol Rev 82(2):e00001-18 (2018)
    4. S. Hathroubi, J. Zerebinski and K. M Ottemann. Helicobacter pylori biofilm involves a multigene stress-biased response, including a structural role for flagella. mBio 9(5):e01973-18 (2018)

Teaching experiences

UCSC_UdeM_HU Berlin
Since May 2018
  • Teaching Molekulare Mikrobiologie (Modul BXY-36,5. Semester)
    Institut für Biologie, AG Mikrobiologie, Humboldt-Universität zu Berlin, Berlin, Germany- 2019-2020 and 2020-2021
    Seminar training, reading and lectures.
    Lectures: Bacterial biofilm and Bacterial pathogenicity
  • Guest lecture microbiology and pathogenesis for undergraduates and graduates: Biofilm, the social life of microorganisms. University of California, Santa Cruz (Winter-Spring session 2018 and 2019)
  • Microbiology and pathogenesis METX 119-02 online, summer session online classes: Biofilm, the social life of microorganisms. Univeristy of California, Santa Cruz (Summer 2018)
  • Teaching course microbial pathogenesis 2 for Master’s degree, veterinary science: Surface polysaccharides and envelope (Part_1. Microbial envelope and Part_2. Surface polysaccharides). Université de Montréal (Fall session 2015)
  • Laboratory demonstrator for Master’s degree, veterinary science students: Basic practical microbiology. Université de Montréal. (2012- 2015)

Mentorship experiences

University of California, Santa Cruz
Since 2017
  • Supervising undergrad student Yasmine E. (University of California, Santa Cruz) - August 2018 - July 2019
  • Supervising Ph.D student Aaron C. (University of California, Santa Cruz) - October 2017 - July 2019
  • Supervising undergrad student Julia Z. (University of California, Santa Cruz) - October 2017-September 2018
  • Supervising summer student Tyler Dewitt (University of California, Santa Cruz) - June-July 2017
  • Supervising student internship Sarah-Eve Fontaine-Gosselin (University of Montreal) Bachelor of Life Science, Sherbrooke University) - January-May 2014

Oral communications

Since 2010
  • Invited Speaker workshop ‘Shelf life, Ferment-Activity’, Berlin; Germany. 10 December 2020

    Invited Speaker workshop ‘Material as Environmental Device’, Berlin; Germany. 10-11 September 2020

    Invited speaker to 5th Workshop on bacterial and fungal biofilms, Ghent University conference Center. May 2019. Unraveling the mystery of Helicobacter pylori biofilm.

    Invited speaker to INRS-INSTITUT ARMAND-FRAPPIER October 2018. Helicobacter pylori biofilm and the unexpected role of flagella.

    Invited speaker to 2nd Technology Seminar-SandBox (UCSC_Startup incubator) September 2018. Targeting the Helicobacter pylori impenetrable biofilm.

    PBSE Research Conference 2018, Felton, California, USA. Unexpected role played by flagella during biofilm formation.

    UC Biosafety officer meeting 2018, Santa Cruz, USA. New Insights into Helicobacter pylori biofilm.

    WCBP Annual conference, 2017, Asilomar, California, USA. Novel genes associated with Helicobacter pylori biofilm growth.

    CRIPA symposium, 2016, St-Hyacinthe, Québec, Canada. Actinobacillus pleuropneumoniae biofilms mitigate innate immune response.

    ASM Biofilm, 2015, Chicago, USA. Actinobacillus pleuropneumoniae biofilms induce lower response of porcine alveolar macrophages.

    CRIPA symposium, 2015, St-Hyacinthe, Québec, Canada. Effect of sub-inhibitory concentrations of penicillin G on Actinobacillus pleuropneumoniae biofilm formation.

    Phd in 180sec (3MTMC) 2014, Science on stage, Faculté de médecine vétérinaire, St-Hyacinthe, Québec Canada. Best presentation 3rd prize. Rôle du biofilm dans la pathogénicité d’Actinobacillus pleuropneumoniae.

    Congrès BiSP 2013, Université Laval, Québec, Canada. Rôle des polysaccharides de surface dans la formation du biofilm chez Actinobacillus pleuropneumoniae.

  • Site-directed mutagenesis (allelic exchange)
    Immunodetection of extracellular polymeric substance (EPS)
    EPS extraction (eDNA...), Immunodot tests
  • Biofilms culture in static and dynamic conditions: Drip flow reactor, BioFlux, MBEC assay, flowCell
  • Enzymatic treatments on biofilms
  • Macrophages in vivo Infection, PBMC isolation
  • Lipid A extractions and structure analysis
  • Microscopies
  • Antibiotic susceptibility tests and serotyping assay of P. aeruginosa clincal strains
  • Static biofilm formation and enzymatic treatments
    Curcumin and berberine chloride test on biofilm
  • Biofilm genes identification
  • Swarming et twitching motility
  • E. coli chromosomal toxin antitoxin systems identification by PCR
    Phylogenetic analyses

2014 to 2016
Canada - Québec
  • Assist students and teachers in location of print and non-print resouces
  • Check books and materials in and out to students and teachers using the computerized circulation system
  • Monitor student use of the library
  • Assist in maintaining the appearance of the library


Université de Montréal
Since September 2012
Canada - Québec
  • Monitoring students during the writing of tests/exams


  • Microscopic identification, biochemical testing of bacteria
  • Antibiotic susceptibility tests and serotyping assay
  • Biofilms culture in static and dynamic conditions
  • Enzymatic and chemicals treatments on biofilms
  • Swarming et twitching motility tests

Cell biology

  • Cell culture, macrophages culture
  • Cytokines detections (PCR and ELISA)
  • PBMC isolation and proliferation
  • Gastric gland isolation and imaging


  • Biofilm staining and EPS detection
  • 3D analysis (biomass, volume and thickness)
  • SEM microscopy of biofilm and flagella detection

Molecular biology

  • DNA and RNA extraction, PCR and RT-PCR
  • Site-directed mutagenesis
  • RNA-seq (Transcriptomic)
  • EPS extraction (eDNA...)
  • Immunodetection of extracellular polymeric substance (EPS)
  • LPS extractions, Lipid A micro-extractions

Animal experiment

  • Mice infection and treatments
  • Gastric gland isolation

PhD in Veterinary Science, Microbiology and Infectious Disease

Faculté de médecine vétérinaire, Université de Montréal

May 2011 to September 2016
Study of micro-organisms in their natural environment. Development of techniques for culturing bacteria form biofilms. Effect of antibiotics on biofilm. Immune response towards biofilms. Phenotypic changes in biofilms cells.
GPA 3.85/4.3


1_Bacterial biofilm derived-antigens: a new strategy for vaccine development against infectious diseases. A. Loera-Muro, A. Guerrero-Barrera, Y. D. N Tremblay, S. Hathroubi and C. Angulo. 2021. Expert Rev of Vaccines

2_ Actinobacillus pleuropneumoniae: Role of biofilm in pathogenicity and potential impact for vaccination development. S. Hathroubi, A. Loera, J.T. Bossé, P.R. Langford and M. Jacques. 2017. Animal Health Research Review. (Published,7:1-14)

3_ Actinobacillus pleuropneumoniae biofilms induce lower response of porcine alveolar macrophages. S. Hathroubi, C. Provost, C. A. Gagnon and M. Jacques. Innate immunity

4_ Biofilms: Bacterial shelters against antibiotics. S. Hathroubi, M.A Mekni, P. Domenico, D. Nguyen and M. Jacques. Microbial Drug Resistance

5_ Surface polysaccharide mutants reveal that absence of O antigen reduces biofilm formation of Actinobacillus pleuropneumoniae. S. Hathroubi, M.A. Hancock, J.T. Bossé, P.R. Langford, Y.D.N Tremblay, J. Labrie and M. Jacques. 2015. Infection and Immunity

6_ Sub-inhibitory concentrations of penicillin G induce biofilm formation by field isolates of Actinobacillus pleuropneumoniae. S. Hathroubi, S-È. Fontaine-Gosselin, Y.D.N. Tremblay, J. Labrie and M. Jacques. 2015. Vet Microbiology (

7_ Les biofilms bactériens : leur importance en santé animale et en santé publique. Y.D.N. Tremblay, S. Hathroubi and M. Jacques. 2014. Canadian Journal of Veterinary Research (
Research Workshop Viral biofilms
Study of Actinobacillus pleuropneumoniae pathogen pork biofilm
Mutagenesis and characterization of biofilm mutant

Communication during PhD program
The "viral biofilms" Out Of Context Seminar
Research Workshop pharmacokinetic / pharmacodynamic

Certificate '' Bacteria biofilms in chronic infections''

Faculty of Health Sciences, University of Copenhagen

September 2012 to November 2012
Distinguish biofilms from planktonic bacteria both in nature and in medical related situations. Examine health care problems caused by infections involving bacterial biofilms. Design and develop biofilm models. Strategies for future research.

Training/Certification program for animal experimentation

Université de Montréal

Since September 2011
The Ethics of animal experimentation gives me the right to experiment on animals ifor laboratory research

Master Applied Microbiology, Environment and Health

Université Pierre Et Marie Curie, Paris 6, France

September 2008 to June 2010
A good understanding of microbiology ; bacteriology, virology, parasitology, environmental quality and health.
Training the Oceanological Observatory Banyuls-sur-mer
Biodiversity and biotechnology to microorganisms

Bachelor of Life Sciences

Université Pierre et Marie Curie, Paris 6 France

September 2005 to June 2008
Scientific knowledge of biology and the general organisation of the animal and vegetable kingdoms as well as the functioning of organisms, from the molecular level to integrated biological systems.


  • Photography; photo treatment Photoshop, ACDSee
  • Adobe InDesign

Foreign trips

  • 18 countries visited
  • Road trips cross-country (Canada, USA)


  • Ethereum (ETH) mining
  • Trading Lumen Stellar, Ripple and Litecoin

La récolte des biofilms_Book participation

B. Beyer and S. Hathroubi. La récolte des biofilms. In: MàJ : design, environnements techniques & pratiques exploratoires. Éditions Cité du design. École supérieure d’art et design Saint-Étienne (ESADSE)/Cité du design, France. 2021

“Active Curtain”_Exhibition “After Nature” at Humboldt Labor at Humboldt Forum_2021

Skander Hathroubi
Humboldt-Universität zu Berlin, 10115 Berlin, Germany
About Me
Ph.D in veterinary science, in applied microbiology, veterinary scientist, microbiologist, microbial biofilm researcher. I was a Junior postdoctoral at University of California Santa Cruz, focusing on survival strategies of Helicobacter pylori, with a particular focus on biofilm and genes associated with this mode of growth. I'm currently a a senior postdoctoral at Humboldt-Universität zu Berlin developing new tools to study morphogenetic movements in macrocolony biofilm.
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