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Skander Hathroubi

Ph.D in veterinary science, microbiologist and biofilm researcher

Skander Hathroubi
Humboldt-Universität zu Berlin, 10115 Berlin, Germany
About Me
Ph.D in veterinary science, in applied microbiology, 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 postdoctoral research assistant at Humboldt-Universität zu Berlin.
  • 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.
  • Investigating Helicobacter pylori biofilm formation and its potential role in pathogenesis in the lab of Dr. Karen Ottemann. I'm using transcriptomic and genetic approaches to identify genes associated with H. pylori biofilm growth. We also use mouse-models for H. pylori infections and imaging approaches (CSLM and SEM) to characterize the biofilm structure its components.

    1. Metabolic changes associated with Helicobacter pylori biofilm. S. Hathroubi, J. Zerebinski and K. M Ottemann (Submitted to npj Biofilms and Microbiomes)
    2. Helicobacter pylori biofilm involves a multi-gene stress-biased response, including a structural role for flagella. S. Hathroubi, J. Zerebinski and K. M Ottemann. 2018. mBio, doi:
    3. Helicobacter pylori biofilm formation and its potential role in pathogenesis. S. Hathroubi, S. L. Servetas, I. Windham, D. S. Merrell, K. M Ottemann. 2018. Microbiology and Molecular Biology Reviews. (published, doi: 10.1128/MMBR.00001-18)

Teaching experiences

Since May 2018
  • 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 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.

Reviser for international Peer-reviewed Journal

Peer-reviewed Journals
Since 2011
  • # Referee/reviewer for Frontiers Microbiology
    # Referee reviewer for Journal of Infection in Developing Countries
    # Referee reviewer for Clinical and Experimental Gastroenterology
    # Referee reviewer for Infection and Drug Resistance
  • Site-directed mutagenesis (allelic exchange)
  • Immunodetection of extracellular polymeric substance (EPS)
  • EPS extraction (eDNA...)
  • Biofilms culture in static and dynamic conditions
  • Drip flow reactor
  • Enzymatic treatments on biofilms
  • Immunodot tests
  • 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
  • Sequencing
  • 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

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


  • 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
  • Drip flow reactor systems
  • MBEC assay

Cell biology

  • Cell culture
  • Macrophages culture
  • Cytokines detections
  • PBMC isolation and proliferation
  • Gastric gland isolation

Confocal microscopy

  • Biofilm staining and EPS detection
  • 3D analysis (biomass, volume and thickness)
  • EPS detection

Molecular biology

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

Animal experiment

  • Mice infection and treatments
  • Gastric gland isolation


  • 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
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