Thematic Project 3: Microbiomes: sentinels of the northern environment and human health
Microbiomes are predominant in the atmosphere, hydrosphere, cryosphere, soils, fauna and humans. The main objective of this thematic project is to determine the roles of microbiomes in the northern human-environment ecosystem by focusing on ecosystems (land, freshwater, seawater), food quality (marine and terrestrial products) and human health (cardiometabolic, respiratory and mental). This broad transdisciplinary collaboration between the fields of physics, chemistry, biology, medicine and engineering will design, develop and deploy new compact instruments for microbiological monitoring in the environment, animal models and humans. The project will also help develop models to assess how important nutritional components such as ω-3 fatty acids are channelled through the Arctic food web.
Specifically, the project will deliver: 1) new photonic sensors for the monitoring of ecosystems, nutrition and health in the North; 2) a better understanding of the coupled human-environment system in the North; 3) new sampling and analysis methods for a wide range of microbiological data in the North, and 4) the training of a new generation of scientists with transdisciplinary expertise to design and apply new photonic technologies for environmental and biomedical applications.
This effort brings together nearly 75 Université Laval professors from 6 faculties, 18 departments and 21 research centers working with numerous international, northern and industrial partners within 8 subprojects.
3.1 Sentinel microbiomes for Arctic ecosystem health
Daniel Côté, Warwick F. Vincent
Claudine Allen, Denis Boudreau, Alexander Culley, Nicolas Derome, Jesse Greener, Connie Lovejoy
Dermot Antoniades, Jacques Corbeil, Patrick Desrosiers, André Marette, Pierre Marquet, Sylvain Moineau, Jean-Sébastien Moore, Mohammed Taghavi
Collaborators outside U. Laval
Abdel El Abed, Anne Jungblut, Weidong Kong, Isabelle Laurion, Rachael Morgan-Kiss, Milla Rautio, Yukiko Tanabe
The Arctic is warming at rates more than twice the global average, and much larger changes are projected for high northern latitudes by the end of this century. This proposal addresses the question: what sentinel microbiome properties of northern marine and freshwater environments can be used to improve surveillance of Arctic ecosystem health in the face of these increasing perturbations? We will harness a broad range of expertise at Université Laval, from molecular biology, chemistry and physics to aquatic ecosystem science, and will extend our scope of activities by collaborating with research centres operating in the Canadian North and with industry. Our first aim will be to identify the composition, complex system properties and resilience of two classes of Arctic microbiomes: planktonic and biofilms. Our approach will harness the power of metagenomics to address knowledge gaps in how to define sentinel microbiomes for the Arctic, and to identify what microbiome properties can be used to determine changes in the health of Arctic ecosystems. We will target: i) environmental microbiomes in a comprehensive set of northern marine and freshwater ecosystems including Baffin Bay, Hudson Bay, lakes and fjords in northern Nunavut and permafrost wetlands in Nunavut; and ii) host-associated microbiomes of the iconic fish species of the North, Arctic char, with emphasis on the impact of both native and invasive pathogenic species on the productivity and sustainability of this major resource. Our second important aim will be to develop two types of novel optical instruments for the central goal of Arctic microbiome surveillance: i) a multimodal opto-fluidics system that can detect and sort specific classes of planktonic cells; and ii) a portable hyperspectral Raman imaging system to quantify microbial biomass via cellular lipids, and to obtain lipid signatures of host-associated and free-living biofilms.
3.2 Comprehensive environmental monitoring and valorisation: From molecules to microorganisms
Michel Allard, Thierry Badard, Alexander Culley, Benoit Gosselin, François Laviolette, Younès Messaddeq, Sylvain Moineau, Dave Richard, Normand Voyer
Patrick Lague, Warwick Vincent
The aim of this research program is to understand how the disruption of ecosystems affects microorganisms in Arctic soils. To achieve our goals, we will use the EcoChip, a microbial in situ culture system for measuring the growth of microorganisms in their natural environment that also enables acquiring and transmitting real-time environmental metadata. The sites under consideration for the deployment of EcoChip span 30 degrees of latitude in the Northern regions and part of the SILA environmental network. We aim to identify sentinel bacteria and investigate how spatiotemporal features affect the microbial consortia. We will design analytical approaches based on integrative genomics, bioinformatics, geolocation and machine learning to quantify the health of Northern ecosystems by measuring in real time these key microbial markers. Our program will enable making predictions of the impact of large-scale environmental changes due to climate change or human intervention on the microorganisms and the functioning of terrestrial ecosystems. In situ analysis of microorganisms with EcoChip will also allow to develop high performance metabolomic models to assess the Nordic molecular diversity and to discover new compounds with potential medical applications including the treatment of tuberculosis. We will therefore use our new high throughput metabolomic mass spectrometry approaches coupled to machine learning in order to accelerate the process of identifying molecules having potential medicinal properties. We will be in a position to exploit the potential of bioproducts for their clinical or industrial uses. With these tools, we will be able to evaluate the impact of environmental changes in the North and effectively add value to the microorganisms found in these environments. At the end of our initiative, we will greatly improve our understanding of the changes occurring in the Northern environments and their impact on human health.
3.3 BriGHT (Bridging Global change, Inuit Health and the Transforming Arctic Ocean)
Jean-Eric Tremblay, Mélanie Lemire
Dermot Antoniades, Philippe Archambault, Pierre Ayotte, Louis Bernatchez, Johann Lavaud, Michel Lucas, Frédéric Maps, Guillaume Massé
Christopher Fletcher, Louis Fortier, Frédéric Laugrand, François Laviolette, Gina Muckle
Collaborators outside U. Laval
Ellen Avard, Michael Kwan, Tommy Pallisser, Kaitlin Breton-Honeyman, Mike Hammil, Véronique Lesage, Shawn Donaldson, Jim Berner , Stig Falk-Petersen, Julien Mainguy, Alphonso Mucci, Gert Mulvad, Frédéric Olivier, CJ Mundy, Tim Papakyriakou, Gary Stern, Feiyue Wang, Pal Weihe
Local marine foods (LMF) are central to Inuit culture and subsistence in the Arctic. Conversely, the Arctic Ocean is changing and Inuit see signs that LMF are different and becoming less accessible. Inuit make food choices according to their preferences but also the accessibility, abundance, visual appearance and quality of different LMF. These four characteristics of LMF are strongly tied to the light environment via the photosynthetic production of microalgal biomass, which is the main entry point for energy, numerous vital or health-enhancing molecules, and contaminants into the food web. Yet we do not know how the quantity and proportion of these substances in algae, zooplankton and LMF respond to climate-driven changes in sea ice, light availability and the physicochemical properties of Arctic seawater, how this response modifies the food choices of Inuit and impacts their health and wellbeing. BriGHT will 1) assess the synergistic effects of light, warming, acidification and nutrient availability on the accumulation of contaminants and the production of health-enhancing molecules in microalgae, 2) model the transfer of these substances from algae to the upper food web, 3) quantify these substances in LMF and the blood of Inuit with respect to their food consumption profiles, the visual appearance of LMF, and indicators of food security, well-being and physical and mental health, and 4) implement novel genomic approaches to monitor spatial and temporal changes in the presence and abundance of LMF. The work will integrate oceanographic sampling, optics, ecosystem modeling and a metagenomic study of Arctic Char foraging in Nunavik, building a synergy with the 2017 Qanuilirpitaa Health Survey. These results will allow to model plausible climate-driven trajectories in LMF characteristics and their likely impact on Inuit health and wellbeing, assisting with the formulation of locally-adapted mitigation adaptation strategies aimed at promoting Inuit local food systems and security in Nunavik.
3.4 Enabling tools for the monitoring of food quality in the Northern environment
Dominic Larivière, Jean Ruel
Pierre Ayotte, André Bégin-Drolet, Denis Boudreau, Jesse Greener, Mélanie Lemire, Gina Muckle
Collaborators outside U. Laval
Ellen Avard, Michael Kwan
The health benefits of country foods from the land, the rivers and the sea as well as the harmful effects of contaminants that may be found in some of them are well documented in Nunavik. However, important aspects of country foods necessitate further study at community level. For example, contaminant levels in lake trout may change from one fish to another depending on location, age and size. A transdisciplinary team gathering U. Laval experts in analytical chemistry, photonic materials, engineering and instrument design, microfluidics, toxicology, psychology and public health, in collaboration with the Nunavik Research Centre, will develop a portable analysis platform for in-the-field testing of various metal contaminants and essential nutrients in country foods. In a second step, partnering with the Nunavik Regional Board of Health and Social Services, we will develop a knowledge user tool to support decision making for local community members and health professionals about the quality of foods in their community. The analysed chemical species will be mercury and lead. The platform will be designed to automatically handle all fluid mixing, optical readout and data logging, making it a user-friendly apparatus, easily operated by untrained personnel. This will be achieved by integrating species-selective capture and chemosensitive photonic materials in microfluidic devices for which the design will have been optimized. The platform and decision making tools will be field-tested and improved upon feedbacks from local community organisations. Fostering local capacities with respect to food analysis and improving access to local information about food quality will enhance Inuit autonomy with respect to food choices and the benefits and safety of their foods and, in the longer term, help to improve food security, health and well-being in Nunavik.
3.5 Impact of environmental conditions on airway microbiota and respiratory health in the North
François Maltais, Marc Ouellette
Pierre Ayotte, Michel Bergeron, Louis-Philippe Boulet, Jean-Pierre Després, Caroline Duchaine, André Marette, David Marsolais, Mathieu Morisette, Barbara Papadopoulou, Roxanne Paulin
Yves Lacasse, Philippe Leprohon, Benoit Levesque, Frédéric Raymond
The aboriginal populations of the North are facing an unprecedented epidemic of respiratory diseases, which is intimately linked to rapidly occurring changes in lifestyle and environmental conditions that have been taken place during the past 20 years. High smoking rates and overcrowded and poorly ventilated homes create a fertile ground for the development of respiratory diseases. Less appreciated is the fact that chronic respiratory diseases often co-exist with cardiometabolic disorders, creating even more complex health problems. The rationale of this proposal is that understanding how the Nordic environment influences the development of chronic respiratory diseases is a crucial step in improving aboriginal health. We hypothesize that modifications in the airway microbiota due to these extreme living conditions provide a plausible link between poor environmental conditions and respiratory diseases. Our objective is to generate crucial information about the impact and development of respiratory diseases in the North that will lead to effective preventive and therapeutic strategies. We will leverage on the 2017 Nunavik Inuit Health Survey (NIHS 2017) that will investigate respiratory health, lifestyle habits, and lung function by i) evaluating the upper airway microbiota of 1000 Inuits aged 18- 30 years and of ≈ 800 participants from the 2004 health survey from the 14 Nunavik communities, and ii) documenting, in a subset of subjects (n = 84) from these two cohorts, the air microbiological environment of their home. Considering that cardiometabolic health and gut microbiota will also be evaluated, we propose to study the interplay between respiratory and cardiometabolic diseases in relationship with the airway and gut microbiota. The clinical investigation will be supplemented by in vivo experimentations allowing to address the research questions in a mechanistic fashion. Knowledge transfer activities and technological development are planned, notably by validating a new method to assess the airway microbiota in a pragmatic way.
3.6 The gut microbiome: sentinel of the northern environment and Inuit mental health
Richard Bélanger, Gina Muckle
Pierre Ayotte, Michel Bergeron, Marc Hébert, Mélanie Lemire, Michel Lucas, Pierre Marquet, Chantal Mérette, Marie-Claude Vohl
Maurice Boissinot, Jacques Corbeil, Christopher Fletcher, André Marette
Collaborators outside U. Laval
Olivier Boucher, Sylvaine Cordier, Mylène Riva
The proposed project is based on findings from previous Nunavik Inuit health survey conducted in 1992 and 2004, which have documented cumulative exposure to adversity among communities (environmental contaminants, food insecurity, victimization, substance use), and high prevalence of psychological distress. Focusing on the 16-30 years old participants from the next population based Nunavik Inuit health survey to be conducted in 2017, this project aims to examine the role of gut microbiome in the association between adversity and mental health. Using the study's global evaluation of health to explore gut microbiome profiles, their association with depressive state will be evaluated using case-control design. The same microbiome profiles will then be link to diverse source and level of adversity lived by young Inuit from Nunavik, but also to several biological markers. As a possible explanation to expected associations, neuronal resiliency specific to Inuit from Nunavik will be explored. As an addition to current efforts taking place in the communities, this project includes in its budget, in addition to a strong transdisciplinary academic plan for students: 1) the collection and analysis of fecal samples used to identify microbiome profiles, 2) the analysis of metabolome and inflammatory biomarkers, 3) the use of electroretinography as an novel indicator of mental health problems and 4) neuronal culture from induced pluripotent stem cells, and 5) the latest and most performing analytical processes. A more comprehensive understanding of mental health problems by integrating involved internal and external environmental aspects of human total exposure is anticipated. Novel markers of adversity, but eventually of psychological distress are projected. Researchers and partners to the project aim to carry both innovation and factors of resilience at the population level.
3.7 Optogenetics investigation of microbiota influence on brain development and epigenetics
Paul DeKoninck, Sylvain Moineau
Daniel Côté, Alexander Culley, Nicolas Derome, Arnaud Droit, Marie-Éve Paquet, Grant Vandenberg
Collaborators outside U. Laval
Robert Campbell, Patrice Couture
The intestinal microorganisms hosted by humans and other vertebrates play a central role in maintaining their hosts in healthy conditions. However, when the host encounters a physiological stress, the microbiota ecosystem equilibrium is broken, allowing opportunistic microbial strains to induce negative effects on the host, including infections and physiological disturbances. During host development, a stressed microbiota might induce significant consequences on its brain development and neural functions, affecting mental health. The Northern ecosystem is undergoing unprecedented assaults from human activities, leading to dramatic environmental changes that are modifying host-microbiota interactions. The relationships between these complex systems are poorly understood. To learn more about host-microbiota interactions and their impact on mental health, we must develop models and tools with which we can accurately control the variables, relevant to the environment, in a laboratory setting. Our objective is to develop a fish experimental model in which we can control factors that modulate host-microbiota functional interactions and measure the impact on microbiota evolution, on brain function, and on host gene expression. Our specific aims are to i) develop molecular tools to study and control microbiota metabolism and growth with optogenetics; ii) develop multispectral optical imaging of the co-evolution of bacterial strains; iii) investigate the impact of nutrition, xenobiotics, phages and bacterial strains on the gut microbiota, on neuronal development and brain circuit function and on epigenetics. The proposed project will involve a transdisciplinary approach combining physiology, optogenetics control and monitoring of gut microbiota, optogenetics monitoring of neural function, as well as genomics and transcriptomics analyses of horizontal gene transfer in bacterial strains, and epigenetics analyses on developing host. The project will lay the foundation of an experimental setting in which several variables critically important to Northern ecosystems will be investigated.
3.8 Deciphering host-microbial interactions for cardiometabolic and mental health disorders with novel multimodal light-based sensing tools
Denis Boudreau, André Marette
Olivier Barbier, Frédéric Calon, Daniel Côté, Vincenzo Di Marzo, Patrick Mathieu, Younès Messaddeq, Denis Richard, Denis Roy, Denis Soulet, Réal Vallée
Mohsen Agharazii, Jacques Corbeil, Yves Desjardins, Nicolas Flamand, Mélanie Lemire, Connie Lovejoy, Anna Ritcey, Elena Timofeeva, Warwick Vincent
Collaborators outside U. Laval
Patrice Cani, Emile Levy
Obesity, cardiometabolic diseases (CMD) and mental health disorders (MHD) are major public health issues among indigenous populations in the Canadian North. It is hypothesized that exposure to various environmental factors, known as the “exposome”, that include changes from a traditional to a more western-type diet, is causing perturbations in the gut microbiome, which may provide a common pathogenic link for the increased prevalence of CMD and MHD in these populations. This new understanding is causing a revolution in the medical field, which is in urgent need of better predictive biomarkers (sentinels) to establish a rapid and efficient diagnostic for these prevalent diseases. We have assembled a new transdisciplinary team of experienced scientists at Université Laval that will transcend the usual academic boundaries and, working together with other prestigious academic institutions and industrial partners, develop and validate new “Sensor-in-Fiber” optical probes using latest advances in fiber optics and photonic materials. These revolutionary opto-microbiomic tools will be implanted in the gastro-intestinal tract of well-established mouse models of CMD and MHD for in situ and simultaneous detection of key microbiome-derived molecules with unsurpassed sensitivity and high spatial and temporal resolution. These novel monitoring tools will allow, for the first time, the sensitive and real-time analysis of the gut microbiota in vivo, leading to the identification of novel microbiome-derived biomarkers and biological targets for a better understanding of the relationship between the exposome and the developmental trajectory of CMD and MHD. The main outcomes of this project are 1) the unprecedented ability to monitor in situ and in realtime potentially novel microbiome-derived biomarkers of CMD and MHD diseases that are relevant to Northern communities, and 2) the discovery of new microbiome mechanisms underlying the health effects of wild berry polyphenols and fish ω3 fatty acids that are traditionally consumed in the North.
Steering Committee for Thematic Project 3
Members of the steering committee:
André Marette, co-director
Department of medicine
Warwick Vincent, co-director
Department of biology
Department of social and preventive medicine
Department of chemistry
418 656-8711, extension 3776
1- Complex systems: structure, function and interrelationships in the North
2- Light as a driver, environment, and information carrier in natural environments and human health
3- Microbiomes: sentinels of the northern environment and human health