Laboratories

Jacek Bardowski, PhD, DSc, Prof.

Laboratory of Lactic Acid Bacteria

Research Scope

Our laboratory is interested in adaptations of lactic acid bacteria (LAB) to different environments they colonize (e.g., plants and the gastrointestinal tract in humans and animals) based on their metabolic potential that is influenced by mobile genetic elements, such as plasmids and bacteriophages. We investigate LAB interactions with other microbes and the human organism. Some of our biomedical and biotechnological applications have been patented.

Research

Main Scientific Achievements

  • We described a new CcpA-dependent, cellobiose-specific PTS system that comprises CelB, PtcB, and PtcA that transports lactose in Lactococcus lactis and found that Man-PTS is a target for the garvicin Q bacteriocin in a broad spectrum of sensitive bacterial genera.
  • We found that two genes (chromosomal AJ89-07570 [big] and AJ89_14230 [prtP]), located on plasmid pIBB477b, are involved in adhesion of the Lactococcus lactis IBB477 strain to components of the gastrointestinal mucosa.
  • We revealed the microbiological composition of complex ecosystems, such as kefir grains, Oscypek cheeses, and spontaneous sourdoughs, based on wholegrain rye, common wheat, and spelt flour.

Research Description

Generally, our research interests concentrate on genetics and mechanisms that regulate gene expression in microorganisms. Our group is involved in research on LAB, with our main focus on such topics as sugar catabolism, plasmidic gene pool in the survival of different stresses, and the isolation and characterization of natural bacterial strains and bacteriophages.

With regard to sugar catabolism, we investigate molecular mechanisms of coupling lactose and b-glucoside catabolism in Lactococcus lactis. This work led us to discover the role of the CcpA protein in the control of lactose metabolism that is induced by cellobiose, which is a plant sugar. Moreover, we discovered new genes and pathways that are involved in lactose catabolism.

We are interested in the enzymatic potential of LAB to degrade various substrates (e.g., starch), which is one of the most abundant carbon and energy sources in nature. Among natural isolates, we collected a few Lactococcus lactis strains that exhibited amylolytic features. One of these was further characterized, showing that the amylolytic enzyme is secreted to the medium and plasmid encoded, and its biosynthesis is regulated by glucose repression.

Another branch of our research deals with the biological diversity of natural bacterial strains and bacteriophages. We isolated several wildtype strains from their natural environment (samples of milk that were collected at farms), and some of them have already been identified and characterized using molecular biology and microbiology methods. Plasmid DNA isolation, analysis, and sequencing were used to characterize the lactococcal plasmidic gene pool that is important for environmental adaptation and for plasmid and strain evolution. A molecular biology approach was applied to characterize isolated bacteriophages. Finally, we developed research on probiotic features of LAB.

Three lines of research recently evolved from our previous studies. One direction is devoted to antagonistic interactions within LAB and between LAB and other microbes. This includes studies of bacteriocins and other anti-microbial substances. A second direction focuses on microbial populations and interactions thereof. It deals with studies of bacterial population diversity and dynamics. A third direction involves studies of molecular mechanisms of LAB bioactivity (including  the biology of LAB bacteriophages) in human and animal organisms in conditions of both health and disease. The importance of these studies is based on ecology and interactions between LAB with other inhabitants of the same environments, industrial agro-food applications of LAB, and the influence of LAB on humans and animals, including a network of interactions within a food-gut-brain axis.

Some of our discoveries that evolved from basic research are being transformed into patents, one of which was licensed, and royalties are continuously enriching the IBB budget until 2027.

Methodology

In our laboratory, we are currently using a large set of classic biochemical  and molecular-based methods:

DNA cloning, polymerase chain reaction, protein purification, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, Western blot, enzyme-linked immunosorbent assays, helicase activity assays, Electrophoretic Mobility Shift Assay (EMSA), phage DNA isolation, phage-sensitivity assays, phage propagation, electron microscopy imaging of phage particles, recombineering tests, cell line proliferation assays, miRNA detection by quantitative real-time polymerase chain reaction, pH/bile salt resistance assays, bacterial adhesion assays, bacteria cultivation using fermenters, microdilution antibiotic resistance assays, and freeze-drying of bacterial cells.

Several specialized methodologies were developed in our laboratory, such as:

  • Method for microbiological growth studies using Bioscreen C (Labsystems Oy, Finland).
  • Phenotype MicroArray Technology for the evaluation of nearly 2000 phenotypes of a microbial cell in a single experiment using preconfigured sets of phenotypic tests that are deployed on microplate panels that contain different classes of chemical compounds that are designed to test for the presence or absence of specific cellular phenotypes.  There are 10 panels that are designed to interrogate metabolic pathways, together with ionic, osmotic, and pH effects, and 10 panels that are designed to assess sensitivity to various antimicrobials with different mechanisms of action (Biolog, USA).
  • Method for the cultivation of bacterial strains under control environmental conditions using BIOSTAT Bplus bioreactors (Sartorius Stedim Biotech, Germany).
  • Method for monitoring the acidification process using a computerized acidifying activity evaluation system (iCINAC, AMS Alliance, Italy).
  • Method for cell disruption using Mini-BeadBeater-8 (16) (BioSpec Products, USA).

List of unique equipment available in the laboratory:

  • Bioscreen C (Labsystems Oy, Finland): System for microbiological growth studies, which incubates, shakes, and measures turbidity (OD) of 200 samples automatically.
  • OmniLog (Biolog, USA): Fully automated Omnilog Phenotype MicroArray that incubates and monitors 50 microplates or 1,920 phenotypic assays simultaneously to measure physiological responses in diverse microbial cells.
  • BIOSTAT Bplus Exclusive Flow|Double Wall (Sartorius Stedim Biotech, Germany): System for animal, plant, and insect cell cultivation and microbial fermentation.
  • iCINAC (AMS Alliance, Italy): System for monitoring acidification activity, which simultaneously observes changes in pH, temperature, and redox potential of one or several samples.
  • Mini-BeadBeater-8 (16) (BioSpec Products, USA): High-energy cell disrupter that disrupts microbial cells and plant and animal tissue by violently agitating up to eight (sixteen) 2 ml screw-cap microvials that contain small glass, ceramic, or steel beads and disruption buffer.

Selected Publications

  • Molecular, physiological and phylogenetic traits of Lactococcus 936-type phages from distinct dairy environments. Chmielewska-Jeznach M, Bardowski JK, Szczepankowska AK*.
    Scientific Reports (Nature), 2018. org/10.1038/s41598-018-30371-3.
  • The Non-Lantibiotic Bacteriocin Garvicin Q Targets Man-PTS in a Broad Spectrum of Sensitive Bacterial Genera. Tymoszewska A, Diep DB, Wirtek P, Aleksandrzak-Piekarczyk T. 2018. Scientific Reports (Nature). doi:10.1038/s41598-017-09102-7.
  • Adhesion of the genome-sequenced Lactococcus lactis subsp cremoris IBB477 strain is mediated by specific molecular determinants. Radziwill-Bienkowska JM, Le DTL, Szczesny P, Duviau M-P, Aleksandrzak-Piekarczyk T, Loubiere P, Mercier-Bonin M, Bardowski JK, Kowalczyk M. Appl Microbiol Biotechnol. 2016. doi: 10.1007/s00253-016-7813-0.
  • Phylogenetic and complementation analysis of a single-stranded DNA binding protein family from lactococcal phages indicates a non-bacterial origin. Szczepankowska AK, Prestel E, Mariadassou M, Bardowski JK, Bidnenko E. PLoS One. 2011. org/10.1371/journal.pone.0026942.
  • Genetic characterization of the CcpA-dependent, cellobiose-specific PTS system comprising CelB, PtcB and PtcA that transports lactose in Lactococcus lactis IL1403. Aleksandrzak-Piekarczyk T., Polak J, Jezierska B, Renault P, Bardowski J. 2011. International Journal of Food Microbiology 2011. org/10.1016/j.ijfoodmicro.2010.12.011.

Collaborations

  • Pierre Renault, Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
  • Elena Bidnenko, Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
  • Baltasar Mayo, Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA) CSIC, Spain.
  • Muriel Mercier-Bonin, Toxalim (Research Centre in Food Toxicology) INRA, Toulouse, France
  • Muriel Cocaign-Bousquet and Pascal Loubiere, Toulouse Biotechnology Institute, INRA,
  • Muriel Thomas and Phillip Langella, INRA, MICALIS, Jouy-en-Josas, France.
  • Libudzisz Zdzisława, Instytut Biotechnologii, Technical University, Łódź, Poland
  • Katarzyna Jagusztyn-Krynicka, Biology Faculty, Microbiology Institute, Warsaw, Poland.
  • Marek Bednarczyk, Life Science University, Bydgoszcz, Poland.
  • Halina Gambuś, Dorota Litwinek and Krzysztof Buksa, Department of Carbohydrate Technology, Faculty of Food Technology, University of Agriculture in Krakow, Poland.
  • Małgorzata Ziarno, Department of Biotechnology, Microbiology and Food Evaluation, Division of Milk Biotechnology, Faculty of Food Sciences, Warsaw University of Life Sciences – SGGW, Poland.
  • Dzung B Diep, Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
  • Rhodia-Food, Olsztyn, Poland.
  • SM Piątnica, Piątnica k/Łomża, Poland

Prizes and Awards

  • Jacek Bardowski. Award of Minister of Since and Higher Eductaion for applied-research activity. 2019. Poland.
  • Magdalena Kowalczyk.James Beard Award in Reference and Scholarship for the collective work edited by Catherine Donnelly. The Oxford Companion to Cheese, encyclopedia, New York: Oxford University Press, ISBN: 9780199330881. 2017. James Beard Foundation, USA.
  • Jacek Bardowski. “Chevalier d’Ordre Palmes Academiques” – Order of the Ministry of National Education of the French Republic, awarded by the French Ambassador in Warsaw, Mr Pierre Buhler, 9 April 2014
  • Kasarełło K, Szczepankowska AK, Bardowski J, Kwiatkowska-Patzer B, Kowalska Z, Lipkowski AW. IMDiK & IBB PAN. Golden Medal Prize at the Warsaw International Exhibition of Innovation 2011 for the invention ‘Lactic acid bacteria for induction of oral tolerance in therapy of multiple sclerosis’. Warsaw. Poland.

Publications

SIEMIANOWSKI K., BOHDZIEWICZ K., SZPENDOWSKI J., KOLAKOWSKI P., ZYLINSKA J., BARDOWSKI J.K., Wpływ zwiększenia zawartości suchej masy w surowcu na teksturę i mikrostrukturę twarogu kwasowego. Acta Agrophysica (2015) 22(2): 183-193 IF -
WYSZYNSKA A., KOBIERECKA P., BARDOWSKI J.K., JAGUSZTYN-KRYNICKA E.K., Lactic acid bacteria-20 years exploring their potential as live vectors for mucosal vaccination. Applied Microbiology and Biotechnology (2015) 99(7): 2967-2977 DOI 10.1007/s00253-015-6498-0 IF 3.337
ALEKSANDRZAK-PIEKARCZYK T., STASIAK-RÓŻAŃSKA L., CIESLA J.M., BARDOWSKI J.K., ClaR—a novel key regulator of cellobiose and lactose metabolism in Lactococcus lactis IL1403. Applied Microbiology and Biotechnology (2015) 99(1): 337-347 DOI 10.1007/s00253-014-6067-y IF 3.337
SZATRAJ K., SZCZEPANKOWSKA A.K., SĄCZYŃSKA V., FLORYS K., GROMADZKA B., LEPEK K., PLUCIENNICZAK G., SZEWCZYK B., ZAGORSKI-OSTOJA W., BARDOWSKI J.K., Expression of avian influenza haemagglutinin (H5) and chicken interleukin 2 (chIL-2) under control of the ptcB promoter in Lactococcus lactis. Acta Biochimica Polonica (2014) 61(3): 609-614 IF 1.389