LAB12

 Plenary Session speakers


JanKokJan Kok

Jan Kok has been a professor in Molecular Genetics in Groningen University since 2004. He has a long-standing expertise in the genetics and molecular biology of Lactococcus lactis, the paradigm starter culture organism for the production of a large range of dairy products. The group of Kok was the first to contribute constitutive and inducible promoters, terminators, signal sequences, low- and high-copy number cloning plasmids, gene expression vectors and single and double cross-over integration strategies to the field of Lactic Acid bacterial research. The vectors and subsequent derivatives are used all over the world, not only in LAB but also in a number of other important (pathogenic) bacterial species. A general emphasis in all his work is on the gene regulatory circuits involved and on examining the circuitry at the whole-genome level (systems biology). Next-generation sequencing (NGS) technology is employed for meta-genome and meta-transcriptome sequencing, for which bioinformatics analyses tools are used and developed in-house. These genome-wide technologies are complemented by techniques such as continuous cultivation for experimental evolution, fluorescence time-lapse microscopy and fluorescence-assisted cell sorting to examine processes at both the population and single-cell levels.

Kok is an ISI Highly Cited Microbiology Researcher with over 220 publications in international refereed scientific journals according to WoS and an h-index of 74 (Google Scholar). A total of 26 PhD students graduated under his (co-)supervision. Also, he is co-inventor on 18 patent (applications) and co-founder of 2 SMEs.

 

 


 

 Douwe van SinderenDouwe van Sinderen

Professor Douwe van Sinderen holds an MSc degree in Biochemistry and a PhD degree (1994) in Molecular Genetics (University of Groningen, The Netherlands). Since 1996 he has been an academic staff member of the School of Microbiology, University College Cork, Ireland, and he currently holds the Chair of Molecular Microbiology. He is also a Principal Investigator of the APC Microbiome Institute, a multi-institutional and cross-disciplinary research centre related to gut health and nutrition, funded by Science Foundation Ireland. Research interests include the comparative genomics and molecular biology of bacteriophages infecting lactic acid bacteria. Furthermore, a significant part of his research activities is dedicated to investigations into comparative and functional genomics of bifidobacteria, which represent common gut commensals of mammals with many reported health benefits. He is a co-author of over 325 peer-reviewed papers, 17 book chapters, editor of 2 books and listed as an inventor on 7 patents.

 


 

Benoit DesguinBenoit Desguin

Benoit Desguin

obtained his PhD in Pascal Hols’ lab in from 2008 to 2013, working on the lactate racemase system of Lactobacillus plantarum. He identified the lactate racemase (LarA) as being a nickel enzyme activated by three accessory proteins LarB, LarC, and LarE and also characterized the aquaglyceroporin LarD, which transports lactic acid and the transcriptional regulator LarR which regulates the Lar locus depending on the enantiomeric excess of L-lactate.

From 2013 to 2015, he went to Robert Hausingers lab at Michigan State University, USA, to pursue the identification of the lactate racemase. During this first post-doc, he identified the cofactor of lactate racemase, the nickel pincer nucleotide (NPN) and characterized its biosynthetic pathway catalyzed by LarB, LarE, and LarC.

Since 2015, he has been back in Pascal Hols lab as Chargé de Recherche FNRS in order to continue the work on the lactate racemase and to explore new NPN-dependent enzymes.

 


 

Jan Peter van PijkerenJan Peter van Pijkeren

Jan Peter van Pijkeren obtained his PhD from the University of Cork for his research on the identification and characterization of surface components of Lactobacillus salivarius. Subsequently, he carried out post doctoral research in the Cork Cancer Research Center and at Michigan State University, before in 2013 becoming an assistant professor in the Department of Food Science, University of Wisconsin-Madison.

His research lies at the interface of industry and medicine, with a focus on lactic acid bacteria. A central part of his research groups activities is the development of genetic tools. Their expertise to efficiently edit the genomes of a variety of lactic acid bacteria species, including probiotic strains, allows them to gain mechanistic insights into probiotic-host interactions. They also exploit their genome-editing expertise to develop tailored probiotics that further enhance the health-promoting properties of these strains.

 


 

Jens WalterJens Walter

Jens Walter is an Associate Professor and Campus Alberta Innovation Program Chair for Nutrition, Microbes, and Gastrointestinal Health at the University of Alberta. After receiving his doctoral degree from the University of Hohenheim in Germany, he performed postdoctoral research into genetic and metagenomic approaches to study gut microbial ecology at the University of Otago in New Zealand. His main research interests are the evolution of vertebrate gut symbionts, basic ecological concepts and how they apply to the gut microbiota, and microbiome targeted nutritional strategies.

 

 


 

kevinVerstrepenKevin Verstrepen

Kevin Verstrepen is professor in Genetics and Genomics at Leuven University and Group Leader in Systems Biology at VIB (Flanders Institute for Biotechnology). He serves as the director of the VIB Center for Microbiology, director of the Leuven Institute for Beer Research and as Honorary Professor at Nottingham University.

Verstrepen studied biological engineering at the Leuven University (KU Leuven) in Belgium. For his MSc thesis, Verstrepen joined Isak Pretorius’ group at Stellenbosch University in South Africa where he studied the genetics of yeast flocculation. His doctoral research at Leuven University was aimed at characterizing yeast genes involved in flavour formation during fermentation. After obtaining his PhD, Verstrepen joined the lab of genetics pioneer Gerald Fink at the Massachusetts Institute of Technology (MIT) in Cambridge, USA. Revisiting the topic of his MSc thesis, Verstrepen discovered that the genes responsible for yeast flocculation contain arrays of highly unstable repeats in their DNA sequence. After spending two years at MIT, Verstrepen joined Harvard University as a Harvard Fellow and group leader. In 2006, he became lecturer and started teaching industrial microbiology to Harvard undergraduate students. Meanwhile, Verstrepen headed a research team dedicated to studying fundamental genetics using yeast cells as a model system. More specifically, building on the previous work, Verstrepen´s team unraveled molecular mechanisms underlying rapid evolution and adaptation. In 2009, Verstrepen returned to Belgium where his team continues to investigate eukaryotic genetics and epigenetics using brewer´s yeast as a model system. In addition, the team is now also focusing on applications in the fermentation industry. In 2012, Verstrepen became managing director of the newly established Leuven Institute for Beer Research (LIBR), a joint research centre that unites different research teams at the university and two associated professional colleges. In 2017, he was appointed as scientific director of the VIB Centre for Microbiology, which groups the different laboratories at VIB that focus on microbiology.

 

 


 

LauraLedesma GarcíaLaura Ledesma-García

Laura Ledesma-García obtained her PhD at Pablo de Olavide University (Spain), she worked on studying the regulatory system that controls the expression of the metabolic pathway implicated in the biodegradation of a xenobiotic pollutant in a Gram-negative bacterium.

Currently, she is post-doc in Pascal Hols’ lab at the Université Catholique de Louvain (Belgium). Her research is focused on understanding of the physiological function of ComRS, one of the major signaling system of streptococci involved in natural competence, predation and biofilm formation.

 


 

Jeroen RaesJeroen Raes

Prof. Jeroen Raes is associate professor at KU Leuven since 2013 and VIB group leader since 2009. His group currently consists of 16 scientists, with expertise in bioinformatics, systems biology, clinical research and microbiology. He has a substantial track record in microbiome research and has been pioneering the analysis and integration of meta-omics datasets (metagenomics, metatranscriptomics, metaproteomics, meta-metabolomics) with environmental, clinical, host omics and dietary data. He was involved in the FP7 MetaHIT and NIH Human Microbiome Project (the latter as only European partner), which laid the foundations for the human microbiome field as it is today. Finally, his lab is performing a wide range of disease-related projects in a.o. IDB, diabetes, cancer, IBS and antibiotics resistance on national (FWO/IWT) funding and develops novel approaches and tools for microbiome research. Jeroen Raes coordinates the Flemish Gut Flora project, a large scale microbiome- focused population cohort in Belgium, and is bioinformatics coordinator in the Tara Oceans project performing large-scale meta-omics analysis of plankton communities.

 


 

Marie Pierre Chapot ChartierMarie-Pierre Chapot-Chartier

Marie-Pierre Chapot-Chartier is Research Director at INRA (Jouy-en-Josas, France). She is the leader of the team “Dynamics of bacterial cell wall” in the MICALIS Institute (Food and Digestive Microbiology for Human Health). After studying physics and chemistry at ESPCI-Paris, she received her PhD in biochemistry from Paris University. She joined INRA in 1989 to work on the proteolytic system of lactic acid bacteria. Since 1994, her main research interests concerned autolysis and cell wall structure of lactic acid bacteria. Her present research focuses on the role of the cell wall components and their structural variations in bacterial physiology and bacteria-host interactions.

 


 

Colin HillColin Hill

Colin Hill has a Ph.D in molecular microbiology and is Professor in the School of Microbiology at University College Cork, Ireland. He has been an SFI Principal Investigator since 2002 (renewed in 2006 and 2010). He is also a founding Principal Investigator in the APC Microbiome Institute, a multidisciplinary research centre focusing on the role of gut microbiota in health and disease. His main interests are in bacteriophage, bacteriocins and the role they play in shaping the microbiome and as interventions capable of preventing infectious disease. He has published more than 480 peer-reviewed papers and holds 15 patents in this area (ISI H factor of 70, Google H factor of 90). In 2005 Prof. Hill was awarded a D.Sc by the National University of Ireland in recognition of his contributions to research. In 2009 he was elected to the Royal Irish Academy, the highest honour for an Irish academic. In 2010 he was elected to the American Academy of Microbiology and together with his colleagues Prof. Gerald Fitzgerald, Prof. Paul Ross and Dr Catherine Stanton he was awarded the Metchnikoff Prize in Microbiology. He served as President of ISAPP (International Scientific Association for Prebiotics and Probiotics) from 2012-2015.

 


 

Ana Rute NevesAna Rute Neves

Ana Rute Neves is the Senior Manager for the Department of Bacterial Physiology & Improvement in the Discovery unit of the Research & Development organization at Chr. Hansen. She is a biochemist with about 20 years’ experience (1996 – 2017) in bacterial physiology and metabolic engineering. Her expertise covers metabolite profiling, fermentation, transcriptomics, genetic engineering and strain development. Rute´s research interests are primarily directed to the identification of factors and understanding of mechanisms that control cellular metabolism in Gram-positive bacteria. In particular the elucidation of molecular mechanisms involved in carbon metabolism have been at the core of her research. The insights gained from these studies provide the firm basis for selection and/or design of strains with desired functional properties. Before joining Chr. Hansen, Rute headed a research group in Bacterial Metabolic Engineering at the Novo Nordisk Center for Biosustainability, Technical University of Denmark (2012-2013), and the Lactic Acid Bacteria & in vivo NMR group at Institute of Chemical and Biological Technology, New University of Lisbon, Portugal (2004-2012). Since she joined Chr. Hansen in 2013, Rute has placed major efforts in implementing systems biology approaches to foster strain development activities.

Rute is a co-author of 56 peer-reviewed publications, has contributed with several oral communications by invitation/selection and is co-inventor of 1 patent. She has coordinated several R&D projects with various national and international collaborations. Rute has supervised over 30 students and researchers in academic settings until 2013 when she joined Chr. Hansen. She acts as reviewer for various peer-reviewed journals, has participated in several scientific evaluation committees and is member of two scientific advisory boards.

 


 

Mariya PetrovaMariya Petrova

Dr. Mariya Petrova is a postdoctoral researcher at the Centre of Microbial and Plant Genetics, KU Leuven and the Laboratory of Applied Microbiology and Biotechnology, Antwerp University, Belgium. In general, her research focuses on investigating genetic, molecular and functional characteristics of lactobacilli involved in host-microbe and microbe-microbe interaction. Currently, she focuses on how vaginal and gastrointestinal lactobacilli can contribute to human health by studying cell wall molecules and their role in colonization, pathogen exclusion, and immune modulation. Also, she is interested in the importance of vaginal and gastrointestinal microbiota during health and disease. Furthermore, she is a member of two scientific advisory boards for conferences focused on probiotics and human microbiome.

 


 

Marco OggioniMarco Oggioni

Marco Oggioni is Professor of Microbial Genetics in the Department of Genetics of the University of Leicester.

 


 

Sigal Ben YehudaSigal Ben Yehuda

Sigal Ben-Yehuda obtained her PhD at the Department of Molecular Microbiology and Biotechnology of the Tel-Aviv University, Israel and subsequently carried out post-doctoral research on the sporulation of Bacillus subtilis in the laboratory of Professor Richard Losick at the Department of Molecular and Cellular Biology of Harvard University, USA. She is currently an Associate Professor in the Department of Microbiology and Molecular Genetics at the Institute for Medical Research, Israel-Canada (IMRIC) in the faculty of Medicine of The Hebrew University of Jerusalem. Her research now focusses on understanding the process of bacterial cell division.

She has received many academic awards including The Sir Zelman Cowen Prize for discovery in medical research (2011) the ISM (Israel society for microbiology)-Shilo Award (2011) and the Hebrew University President’s Award (Ben-Porat) for excellence in research (2007).

 


 

Joyce MulderJoyce Mulder

After obtaining her BScc degree, Joyce completed her MSc education in 2014 at the Vrije Universiteit Amsterdam with 2 specializations: molecular cell biology and biological chemistry. Currently, she holds a position as a PhD student at NIZO/Rijksuniversiteit Groningen within the BE-Basic consortium. In this project, she studies horizontal gene transfer in lactic acid bacteria. This work has resulted in a publication on induction of natural competence in Lactococcus lactis which is the subject of the oral and poster presentation.

 


 

Herwig BachmannHerwig Bachmann

Herwig Bachmann obtained his PhD at Wageningen University on the behavior of lactic acid bacteria in a dairy environment, which he investigated using molecular tools, -omics technologies and evolutionary engineering. He has developed protocols for high-throughput, in-product screening and for the selection of organisms with increased biomass yield. Besides leading the fermentation expertise group at NIZO he is also project leader at the Top Institute Food and Nutrition and holds a part-time position as an assistant professor at the Vrije Universiteit Amsterdam. The current focus of his work is on microdroplet based technologies to increase the product yield in fermentation based processes and on evolutionary trade-offs in microbes.

 


 

Stefania ArioliStefania Arioli

Stefania Arioli is currently a post doctoral fellow at the Department of Food Environmental and Nutritional Sciences (DeFENS, University of Milan), with a project titled “Study on probiotic properties of Lactobacillus paracasei strains” (Project advisor: Prof Simone Guglielmetti).

Dr Arioli obtained her PhD degree in 2009, at the University of Milan, discussing the thesis titled “Carbon dioxide metabolism in Streptococcus thermophilus: physiological and ecological importance and dairy applications”.

Dr Arioli has been awarded by Italian Society of General Microbiology and Microbial Biotechnologies (SIMGBM) for the best PhD thesis in microbial biotechnologies (2009); by the Italian Society of Agro-Food and Environmental Microbiology (SIMTREA) for the best oral presentation (2012) during the National Conference of SIMTREA (Bari, Italy). She has been awarded by SIMTREA for the publication “Microbial urease in health and disease” (by Arioli S and Mora D, PLOS Pathogen, 2014). Dr Arioli received a grant from SIMTREA in 2017 for funding a project titled “Flow cytometry for studying on impact of moderate heat, carvacrol, and thymol treatments on the viability, injury, and stress response of Listeria monocytogenes”. Dr Arioli is author/co-author of 43 publications, focused on metabolism and physiology of lactic acid bacteria (LAB), antibiotic resistance in food associated bacteria, selection and characterization of new probiotic strains, and development of flow cytometry-based applications for the enumeration and the evaluation of the physiology of LAB andprobiotics

 


 

Marco VenturaMarco Ventura

Marco Ventura is Associate Professor at the University of Parma, Italy. He received his Ph.D. in Natural Sciences at the Swiss Federal Institute of Technology (ETH) Zurich, Switzerland, in 2003. He did postdoctoral research work at the Dept. of Microbiology, National University of Ireland, Cork (Ireland) before joining the faculty at the University of Parma in 2005. His research is focused on the molecular analysis of bifidobacteria, as well as the diversity and host significance of the gut microbiota.

 


 

Richard LenskiRichard Lenski

Richard Lenski is the John Hannah Distinguished Professor of Microbial Ecology at Michigan State University. He studies the genetic mechanisms and ecological processes that cause evolution. In an experiment started almost 30 years ago, he and his team have followed 12 populations of bacteria as they have evolved in the laboratory for over 65,000 generations, providing insights into the process of adaptation by natural selection, the dynamics of genome evolution, and the origin of new functions. Samples throughout the experiment are stored in a freezer, and the organisms that lived in different generations can be revived and directly compared—in effect, time travel.

Prof. Lenski is past President of the Society for the Study of Evolution, and he was a member of the National Research Council committee that reviewed the scientific approaches used in the FBI’s investigation of the 2001 anthrax attacks. He helped found the BEACON Center for the Study of Evolution in Action, which brings together biologists, computer scientists, and engineers to illuminate and harness the power of evolution. Prof. Lenski is a member of the US National Academy of Sciences and an associate member of EMBO. He has mentored some 25 graduate students and postdoctoral associates who are now on the faculties of universities around the United States and the world.

 


 

Ana SolopovaAna Solopova

After graduating in 2009 as an MSc (Cum Laude) in Microbiology at Vilnius University, Lithuania, Ana Solopova worked on the phd project on the identification of the mechanisms that underlie various lag-phases occurring during substrate-shift of bacterial cultures and the assessment of the role of population heterogeneity in these processes using a lactic acid bacterium, Lactococcus lactis, as a model organism at the Molecular Genetics Department of the University of Groningen, The Netherlands. She is currently a researcher in the same department. Her research work involves the metabolic engineering of L. lactis for high-value plant phenolics production, metabolic biosensor development and use and also manipulation of host metabolic networks.

 


 

MaryO ConnellMotherwayMary O'Connell Motherway

Mary O'Connell Motherway is a Research Fellow and Faculty Member of the APC Microbiome Institute at University College Cork. Mary’s specialises in Comparative and Functional Genomics of Probiotic bacteria and in particular Bifidobacteria.

 


 

Christoph BoltenChristoph Bolten

Christoph J. Bolten received his PhD in Industrial Microbiology (Bio-based Production of L-Methionine in Corynebacterium glutamicum) from the Technical University of Braunschweig, Germany. Afterwards he did a post doc on Metabolic Network Analysis of Plant Systems. In 2010, Christoph Bolten joined the Nestlé Research Center as a project manager and scientist in the field of biotransformation. Following roles as Salt Reduction Team Leader and Research & Development Interface Leader, he took the lead of the Technical Microbiology group. The team hosts the Nestlé Culture Collection of more than 3000 food grade strains and focuses on delivering natural solutions for various business units via the development of new fermentation processes and the identification of novel enzymes as well as probiotics.

 


 

Bernard MoongaBernard Moonga

Is a PhD candidate in the Laboratory of Food Microbiology at Wageningen University. He holds an MSc in Food Technology from Gent University/KU Leuven and a BSc in Agriculture from the University of Zambia (UNZA). He works as a lecturer at UNZA where he has served since 2004 in the Department of Food Science & Nutrition and has been Head of Department from 2008 to 2012. He teaches courses in Food Fermentation, Dairy Technology and Fruit & Vegetable Processing. He has been involved in several research projects some of which include: product development of sorghum based products and fruit-whey beverages, increased utilization of cowpea for improved health benefits, nutritional value of African indigenous vegetables as well as microbiological safety of opaque beer and meat sold outside the cold chain. His current research interests are on traditional fermented milk, “mabisi” from Zambia which is aimed at determination of microbial communities, starter culture development and product optimisation.

 


 

Maria Elena MartinoMaria Elena Martino

Maria Elena Martino is post-doctoral researcher at the Institute of Functional Genomics of Lyon (France). Her research interests lie in understanding the processes underpinning the evolution of bacteria and their adaptation to new environments. She is currently working on deciphering the genetic mechanisms of the mutualistic interaction between bacteria and their hosts, to understand the molecular basis of microbial benefit towards host growth.

 


 

Philippe Langella

Philippe Langella is Leader of the Laboratory of Commensals and Probiotics-Host Interactions at the MICALIS Institute, INRA, Jouy en Josas, France.

 


 

 Takahiro MatsukiTakahiro Matsuki

Takahiro Matsuki graduated from the Faculty of Science, Tokyo Institute of Technology in 1992. After completing his master’s course at the Tokyo Institute of Technology in 1995, he joined the Yakult Central Institute. From 1996 to 1999 he was a visiting scientist at the University of Tokyo. He obtained his PhD at the University of Tokyo in 2005. He was a visiting scientist at Institute Pasteur from 2008 to 2010. His major fields of study are the molecular ecology of human gut microbiota, bacteriology and genome microbiology. He is a member of the editorial boards of FEMS Microbiology Ecology, Beneficial Microbes and Bioscience of Microbiota, Food and Health and is an academic committee member of Bifidus Foundation. He was awarded the Kuroya Prize by the Japanese Society for Bacteriology in 2007.

 


 

Hanne JouhtenHanne Jouhten

Hanne Jouhten obtained a Bachelor of Science (Food Microbiology) from the Faculty of Agriculture and Forestry, University of Helsink in 2015. Her BSc thesis was a review about effects of early microbial contacts on gut microbiota development and health. She obtained a Master of Science (Microbiology) from the same university Faculty of Agriculture and Forestry, University of Helsinki, with her thesis entitled “Binding of fecal bacteria to Caco-2 cell line as a pre-selection step in isolating commensals with potential to inhibit Clostridium difficile adhesion”. She is currently a PhD student in the Doctoral Program in Biomedicine at the Faculty of Medicine, University of Helsinki researching the long term changes of recurrent Clostridium difficile infection-patients’ gut microbiota and resistome after a fecal microbiota transplantation.

 


 

Jun ChenJun Chen

Jun Chen has a PhD in Microbiology from the Department of Systems Biology of the Technical University of Denmark, Lyngby, Denmark and is currently a researcher at the National Food Institute in the Technical University of Denmark. He is studying bacterial physiology and metabolism developing techniques for droplet high-throughput screening for improving functionalities of microbes and performing metabolic engineering of bacteria to produce food ingredients and chemicals.

 


 

Patrick VeigaPatrick Veiga

Patrick Veiga received his PhD from the Université of Orsay - Paris XI in 2007. His doctoral research was focused on identifying genes contributing to the synthesis or the modification of the Lactococcus lactis cell wall; under the supervision of Dr. Saulius Kulakauskas (Institut National de la Recherche Agronomique, Jouy-en-Josas, France). After a one year post-doc at INRA Thiverval-Grignon during which he studied the regulation of the carbon metabolism of Bacillus subtilis using a system biology approach, he joined the newly created “Gut Flora” science team of Danone Research in 2008 with the mission to investigate the interplay between probiotics and gut microbiota, an emerging field at that time. In 2011, he was assigned as a visiting scientist to the Lab of the Prof. Wendy Garrett (Harvard School of Public Health) in Boston (MA) where he spent 3 years identifying the “probiotic effectors” of a commercial product and their effects on the host immune system. In 2014, he took the position of Gut Microbiota Research Axis co-leader within the Life Science (LS) Dept of Danone Nutricia Research (Palaiseau, France). Lately (2017), he was appointed Head of the “Microbes & Foods for Health” science team and Scientific Advisor for the Dairy Division, a position that entails the lead of the Life Science Dpt scientific strategy of the Dairy division.

 


 

Eveline BartowskyEveline Bartowsky

Eveline Bartowsky is Applied Microbiologist at Lallemand Australia. She provides the Australian and New Zealand wine industry with technical microbiological and fermentation support and oversees winemaking trials. Previously, Eveline was a Senior Research Microbiologist at The Australian Wine Research Institute leading the bacterial research team and Manager of the AWRI Wine Microorganism Culture Collection. She has over 23 years’ experience in wine microbiology with research interests focused on wine bacteria and malolactic fermentation, wine aroma and flavour, yeast and polyphenolics interactions and minimising wine spoilage by lactic acid and acetic acid bacteria.

Following a PhD in microbiology from The University of Adelaide, Eveline undertook postdoctoral studies in Sweden (Umeå University, Umeå), USA (Washington University Medical School, St. Louis) and University of Adelaide. She has wide experience with a diverse group of bacteria: Vibrio cholerae, Citrobacter freundii, and wine associated Lactic Acid Bacteria and Acetic Acid Bacteria. In addition, she worked as a Research Fellow on the biological control of stored product pests, investigating the molecular basis of the immune response of parasitic wasps and their moth host (University of Adelaide).

Eveline is world recognized for her research into wine bacteria and has published over 100 papers including journal articles, book chapters and technical papers.