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Skander Hathroubi

Ph.D in veterinary science, microbiologist and biofilm researcher

Skander Hathroubi
Biofilms
Microbiology
Veterinary science
Helicobacter
Pathogenesis
Contact
+4917631696388 skander.hathroubi@hu-berlin.de
Humboldt-Universität zu Berlin, 10115 Berlin, Germany
About Me
Ph.D in veterinary science, M.sc 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.
Experience
  • 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
  • https://www.matters-of-activity.de/en/members/233/skander-hathroubi-phd
  • Teaching Molecular Mikrobiologie Modul BXY-36. Wintersemerster (2019-2020)
  • Guest lecture: Biofilm microbial shelters. Feb. 2020. Humboltd-Universität zu Berlin
  • 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 AEM) https://www.biorxiv.org/content/10.1101/728766v1)
    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: https://doi.org/10.1101/412239.
    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

UCSC_UdeM
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

Conferences
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

Webmaster

www.bacterialbiofilms.com
2014 to 2016
Freelancer
SAINT HYACINTHE
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

Proctor

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

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

Publications:

1_ 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)

2_ Actinobacillus pleuropneumoniae biofilms induce lower response of porcine alveolar macrophages. S. Hathroubi, C. Provost, C. A. Gagnon and M. Jacques. Innate immunity
(http://www.ncbi.nlm.nih.gov/pubmed/27226465)

3_ Biofilms: Bacterial shelters against antibiotics. S. Hathroubi, M.A Mekni, P. Domenico, D. Nguyen and M. Jacques. Microbial Drug Resistance
(http://www.ncbi.nlm.nih.gov/pubmed/27214143)

4_ 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
(http://www.ncbi.nlm.nih.gov/pubmed/26483403).

5_ 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 (http://www.ncbi.nlm.nih.gov/pubmed/26130517).

6_ 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 (http://www.ncbi.nlm.nih.gov/pubmed/24688172).
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.
Project communication: GENOTYPIC AND PHENOTYPIC CHARACTERIZATION OF BIOFILM PRODUCTION IN PSEUDOMONAS AEROGINOSA STRAINS IN THE BONE MARROW TRANSPLANT CENTER OF TUNIS, TUNISIA
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.
Skills

Microbiology

  • 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
Interests

Informatics

  • Photography; photo treatment Photoshop, ACDSee
  • Adobe InDesign

Foreign trips

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

Cryptocurrency

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