The Canadian Society of Microbiologists - Meet The Microbiologist

Taking on superbugs with new insights into uncharted biology

Eric Brown - McMaster University — Tue, 12 Jun 2012 08:00:00 EST

Multidrug resistant bacteria continue to be a health-care burden in both hospital and community settings. Remarkably, in the past fifty years, only a few new chemical classes of antibiotics have reached the clinic. Existing antibiotics are directed at a small number of targets, principally cell wall, DNA and protein biosynthesis. Indeed, multidrug resistance among bacterial pathogens is thought to be due in large part to the limited repertoire of antibacterial chemical matter that eradicate bacteria using a narrow range of mechanisms. Bacterial genomics heralded a genes-to-drugs approach where new targets would lead to new chemical matter that inhibit bacterial growth with new mechanisms of action and are unsusceptible to existing resistance mechanisms. Unfortunately, there have been no new drugs with this approach. Among the most significant obstacles to modern antibacterial drug discovery has been a struggle to understand the complexity of the biology that underlies various targets. In efforts ongoing, the Brown Labresearch group is working to explore largely uncharted aspects of complex biology in bacteria. We are working to comprehend poorly understood aspects of cell wall biosynthesis, in particular the biogenesis of wall teichoic acid in Gram-positive bacteria. We are also characterizing conserved and enigmatic proteins that have vital roles in the assembly of ribosomal subunits in bacteria. Further we have embarked on ambitious efforts to uncover new chemical probes of bacteria and to chart chemical-genetic interactions for known and novel antibacterial compounds on a genomic scale. Together the ultimate goal of these studies is to contribute to fresh directions for new antibacterial therapeutics.

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Microbial Diversity Explorations

Josh Neufeld - University of Waterloo — Fri, 4 May 2012 08:00:00 EST

Distributions

For most of Earth's history, microbes have governed the cycling of carbon and nutrients, contributing to nearly all of the genetic and metabolic diversity present within today's planetary biodiversity. Exploring this microbial diversity in aquatic, terrestrial and host-associated environments, my lab has three main research foci. Firstly, we develop and apply methods for investigating the taxonomic diversity of microbial communities, trying to understand how these communities are structured in relation to, for example, environmental disturbances or human diseases. Importantly, we are developing computational and molecular methods for revealing the identity and functions of microorganisms that exist at low relative abundance (i.e. "the rare biosphere") and have escaped detection by previous methodologies.

Metagenomics

We link the ability of active microorganisms to assimilate carbon sources with their genomic information using incubations with stable-isotope labelled compounds (e.g. stable-isotope probing; SIP).These ongoing studies have potential applications for industry given that we are now focusing on retrieving novel glycosyl hydrolases from microbes that consume important substrates such as cellulose and other plant-derived carbon compounds.

Biogeochemistry

My lab investigates nitrogen cycling in aquatic and terrestrial environments. For example, we are now studying the poorly understood role of Archaea in oxidizing ammonia in engineered environments by combining both cultivation dependent and cultivation independent approaches.

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Microbial diversity and function in aquatic and wastewater systems

Andrea Kirkwood - University of Ontario Institute of Technology — Mon, 18 Jul 2011 08:00:00 EST

The Role of Microbial Food-webs in Aquatic Ecosystem Function

To improve our understanding of energy flow and nutrient cycles across freshwater ecosystems, the long-term research objectives of the Kirkwood lab are to assess the structure and function of microbial food-webs, including a focus on the microbial loop as the engine of carbon and elemental nutrient flux. Concurrent with these long-term research foci, we will investigate the role of the microbial loop in controlling contaminant fate in surface waters. In the near-term, our research program is focusing on the roles of algae and bacteria as key players in aquatic ecosystem function and contaminant fate. Specifically, our research group is determining how the synergistic and antagonistic interactions between algae and bacteria mediate carbon, nutrient, and contaminant dynamics in lakes of The Land Between. This project has the capacity to support both Masters and Ph.D. projects, so please contact Dr. Kirkwood if you are interested in pursuing this area of research for your graduate studies.

Microbial Diversity and Function in Urban Aquatic Systems

Aquatic systems (i.e. ponds, creeks and wetlands) in urban environments are classically viewed as biologically depauperate, with minimal ecological function. However, as microbial ecologists know, microbial communities in even the most extreme environments can be surprisingly diverse. We are investigating the role of microbes (algae and bacteria) in the ecological function of urban ponds and wetlands. Current studies include: (1) An examination of the capacity of different urban wetland types to tolerate and biodegrade chlorinated contaminants; and (2) The characterization of urban storm-water ponds with respect to water quality parameters, contaminants and microbial diversity and activity.

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Molecular Mechanisms of Multidrug Resistance in Gram-Negative Bacteria

Ayush Kumar - University of Ontario Institute of Technology — Fri, 29 Apr 2011 08:00:00 EST

Antimicrobial resistance of bacterial pathogens is one of the biggest challenges we face today in the field of microbiology. Many bacterial cells have gained resistance to every single class of antibiotic in clinical use, often making treatment options very limited. One of the key mechanisms of intrinsic antibiotic resistance of Gram-negative bacteria is through the activity of multidrug efflux pumps belonging to the Resistance-Nodulation-Division (RND) family. These proteins are capable of pumping out various structurally-unrelated antibiotic molecules against the concentration gradient, using the proton-gradient as an energy source. RND pumps have been shown to be responsible for multidrug resistance of a number of Gram-negative bacterial pathogens, and it is becoming increasingly clear that a better understanding of the function and regulation of these pumps is essential in order to design novel and more effective therapeutic measures.

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Genetics and Molecular Pathogenesis

Brian Coombes - McMaster University — Wed, 20 Apr 2011 08:00:00 EST

Just as humans inherit certain traits from generation to generation, the same is true of bacteria that inherit genetic information from their ancestors. This genetic information specifies not only what type of bacteria it will become, but also how it interacts with its surroundings, whether it will be pathogenic or not, and whether it is resistant to certain antibiotics. For each gene in its genome, a bacterial cell controls where and when genes are expressed by integrating environmental cues with signaling cascades leading to transcriptional activity. By sensing their surroundings, bacteria can turn genes on or off at certain times, or produce more of a certain gene product when it is needed most, allowing them to rapidly respond to their environment and exploit the immediate surroundings, such as in a human or animal host.

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Cave Microbiology, Antibiotic Resistance, and Microbiology Teaching

Naowarat Cheeptham - Thompson Rivers University — Wed, 16 Mar 2011 08:00:00 EST

Antibiotic resistance in pathogens is surfacing at an increasing and alarming rate in hospitals and communities around the world. My research has primarily centered on microbial diversity, microbial secondary metabolites production, and searching for potential natural products and bioactive compounds. Research questions our group is after for answers have focused on whether new drugs with different mode of actions and with new scaffolds can be found in rare/less-intensive-studied microorganisms living in extreme habitats (i.e., in caves)?

Besides, my own disciplinary research in cave microbiology and antibiotic resistance mechanisms, I am very much interested in how students learn and pedagogically what can help them understand microbiology. In 2009, I was selected as one of the biology research residency scholars in the ASM/NSF Biology Research Residency Scholars Program and participated in an NSF-sponsored residency to improve my understanding and practice of evidenced-based teaching and learning. This undertaking is a multiyear leadership program for college/university biology faculty to bring about reforms in undergraduate science education and it focuses on developing biologists’ knowledge and skills in evidenced-based research in learning.

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Exploration of host specificity and virulence of an opportunistic human pathogen

John Stavrinides - University of Regina — Fri, 25 Feb 2011 08:00:00 EST

Understanding pathogen host range, genetic determinants of virulence, and the evolutionary processes that contribute to pathogen diversification and host-specific adaptation are essential for predicting, controlling, and preventing emerging and reemerging infectious diseases. This is especially true for bacterial pathogens that are not generally considered human pathogens, but exhibit the capacity to cause human disease.

Pantoea is a relatively recently defined genus within the Enterobacteriaceae – a group of bacteria that comprises animal-pathogenic species including E. coli, Salmonella, and Yersinia. Despite their close relationship to animal pathogens, species of Pantoea have been studied primarily from the perspective of their plant pathogenic and plant epiphytic lifestyles. Over the last decade, however, members of the genus Pantoea have been isolated recurrently in the clinical setting where they have been found causing severe infections, and have even been linked to many human fatalities. The Center for Disease Control reports that the Enterobacter/Pantoea group is responsible for almost 17% of hospital-acquired and pneumonia isolates, and members of this group are the single most frequently isolated Gram-negative organism in intensive care unit bloodstream infections. These strains are also the third most common pathogen isolated in intensive care unit cases of pneumonia, and have a fatality rate of 12.5%. Many of these clinical isolates of Pantoea have been shown to be closely related to plant and environmental strains, raising questions about whether all strains have human pathogenic potential.

My research lab uses a combination of genetic, genomic, and evolutionary approaches to understand the relationships between strains, their host specificity, and the underlying evolutionary forces that drive the formation of new host associations. My research group is currently exploring the pathogenic potential of different isolates of Pantoea using model plant, insect, and animal hosts, and we are combining this with various genetic screens to identify host-specific virulence factors. Comparisons of host colonization of different strains and mutant lines can provide important insight into the roles of specific genetic determinants in disease development. The images shown depict the colonization of insect tissues by fluorescently-labeled pathogenic bacteria. In addition, we are taking a comparative genomic approach to understand the relationships between clinical, environmental, and plant isolates of Pantoea, and whether there are specific determinants that enable particular strains to be pathogenic to humans.

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Undergraduate Microbiology Teaching

Jessica Boyd - American University of Nigeria — Wed, 23 Feb 2011 08:00:00 EST

I have recently shifted my career away from research towards teaching microbiology to undergraduate university students. I think it critical that today’s biology students understand the influences microbes have on their own health and the world around them from immunology to global warming. I am working to increase the profile of microbiology at the undergraduate level.

I am currently teaching part time at St. Mary’s and Mt. St. Vincent Universities in Halifax and looking for permanent employment in Canada and abroad.

Previous research explored bacterial pathogenesis, genetics and genomics. Some projects were: an exploration of the virulence factors the bacterium Aeromonas salmonicida uses to infect and kill Atlantic salmon; and analysis of the transcriptional regulation of the pilus genes of the human opportunistic pathogen Pseudomonas aeruginosa.

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Understanding how Salmonella establishes infection in humans

Nancy Martin - Queen''s University — Wed, 23 Feb 2011 08:00:00 EST

Salmonellabacteria are responsible for two diseases that significantly impact human health: typhoid fever and salmonellosis. While S. typhi, responsible for typhoid fever, has been largely eradicated in developed countries, the World Health Organization's estimate of the number of infections is 17 million individuals worldwide annually, with a minimum death toll of 600,000. Salmonella species responsible for gastric salmonellosis in humans cause annual infection rates that are high in many countries, with fatality rates among the very young and immunocompromised as high as 25% of infected persons in some areas of the world.

Many Salmonella species are resistant to antibiotics and a single strain is often resistant to multiple drugs, making treatment with antibiotics very challenging. My research program focuses on revealing the mechanisms by which Salmonella invades host cells in order to understand the body's immunological response and help to isolate effective vaccines. In light of our dwindling supply of effective antibiotics, vaccine development against Salmonella is an important approach to improving human health.

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Organic pollutant biodegradation

Jonathan Van Hamme - Thompson Rivers University — Wed, 23 Feb 2011 08:00:00 EST

Bacteria and other microorganisms are well known to play a critical role in the biodegradation and detoxification of organic pollutants in natural ecosystems. Exploiting and managing these natural roles to remediate contaminated environments, and having an understanding of the microorganisms involved in these processes, is essential for designing engineered solutions to pollution problems. Further, microbial processes are often used for the production of fine chemicals and pharmaceuticals thanks to the metabolic versatility and diversity of this group of organisms. We aim to expand our knowledge of the molecular and biochemical nature of bacterial transformations of sulfur-containing organic contaminants by bacteria and fungi using traditional, genomic and proteomic approaches. We hope to develop biocatalysts and biosensors for bioremediation of contaminants such as mustard gas hydrolysis products, sulfonated Perfluorochemicals and petroleum hydrocarbons. Significant stores of mustard gas remain in storage depots in the US and aquatic dump sites in Canada and abroad, a legacy remaining from WWI. Perfluorochemicals are emerging toxic contaminants used in the manufacture of products such as water and stain repellents, non-stick coatings, and some firefighting foams. Finally, we have recently begun exploring the impacts of feed additives on methanogenesis and fecal E. coli shedding from cattle.

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Agriculture, Microbiology, the Environment, and Human Health

Edward Topp - Agriculture and Agri-Food Canada — Tue, 22 Feb 2011 08:00:00 EST

One of humanity’s great challenges is to feed the growing world population. Fortunately, Canada is one of the Earth’s great “breadbaskets”. This country’s agriculture and agri-food system generates about 8% of the total Gross Domestic Product, and provides about one in eight jobs, a hugely important sector of the national economy. About 6% of the Canadian territory is farmed to grow crops and livestock, and much of the production is in proximity to water resources whose quality is important to both citizens and wildlife. Within this context, our team conducts research to evaluate and to devise means of managing the risk to water from contaminants generated in agricultural production. Our specific interests concern the ecology of enteric microorganisms in the agro-ecosystem; the fate of veterinary and human drugs following the application of manures or biosolids to soils; and the impact of agricultural production practices on the development of bacterial resistance to antibiotics. In partnership with numerous national and international collaborators, our experimental work is undertaken from the bench to the watershed scale. We utilize both conventional and molecular means to detect, enumerate, isolate and characterize indicator and pathogenic microorganisms obtained from environmental matrices impacted by agriculture. The sources of enteric pollution are elucidated at policy-relevant scales, and environmental bacteria are characterized with respect to human health risk. The microbial basis for the biodegradation in soils of pharmaceuticals, hormones and other organic chemicals of anthropogenic origin is investigated. Information from these studies is used to help inform the development of agricultural practices and policies that are protective of environmental quality and human health.

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Using Bacterial Genetics to Study an Important Bacterial Symbiont of Plants

Christopher Yost - University of Regina — Thu, 27 Jan 2011 08:00:00 EST

Globally, nitrogen fixation involving symbiotic rhizobia is the major source of nitrogen input for many important food crops, such as peas, lentils, soybeans and chickpeas. The rhizobia represent an excellent model system for investigating questions of fundamental biological significance, such as understanding the molecular mechanisms required for a cell to adapt to diverse conditions, both in the soil and during infection of a host plant. The objective of my research program is to identify and characterize cell envelope genes and regulatory pathways that are required to modulate the composition of the cell envelope during Rhizobium leguminosarum's adaptation to varying soil conditions, and during plant infection. The cell envelope is an interesting target for studying bacterial adaptive responses to stress since it is the first line of defense against external stresses and maintaining its integrity is a prerequisite for survival within the external environment as well as a host. For example, we are interested in understanding how R. leguminosarum modulates the cell envelope to survive environmental stresses, such as drought induced desiccation. My lab uses a genetics based approach to identify genes that are important for the function and maintenance of the cell envelope. Using this approach we have identified several uncharacterized genes that appear to be important for proper cell envelope function and cell morphology. Examples of mutants with unusual cell morphologies are shown in the accompanying transmission electron microscope picture. The mutant is shown in panel A and wildtype is shown in panel B.

R. leguminosarum fixes nitrogen for several important food crops that are grown on the Canadian prairies including peas, and lentils, and predictions estimate that by 2028, 1/3 of the annual crop base in the prairies will be in these pulse crops. In spite of this, relatively little is known about this agriculturally important Rhizobium species. A better understanding of how R. leguminosarum modulates the cell envelope to survive in soil and during infection can help agri-biotech industries create more effective inoculants designed to increase legume crop production for Canadian farmers. Furthermore, Canada is a global leader in the agricultural biotechnology sector and the students receiving training in my lab develop skills in molecular based approaches that are sought after by agri-biotech employers, positioning them well for future employment in this expanding sector.

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