A collaborative team of researchers (Drs. Kieran O’Doherty, Rob Beiko, Sue Ishaq, Emma Allen-Vercoe, Mallory Choudoir, and Diego Silva – check out their biographies below) has been awarded funding from the Canadian Institutes for Health Research (CIHR) for a four-year project on how our collective microbiomes (the diverse microbes we share between humans and our environments) impact health!! 

Microbiome scientists have increasingly been demonstrating the importance of microbial ecologies for human and environmental health. In spite of this, no protections are in place on policy levels to ensure the health of microbiomes, which in turn are the foundation of larger ecosystems.  We built this team of bioethicists (Kieran and Diego), bioinformaticians (Rob), host microbial ecologists (Sue and Emma), and soil microbial ecologists (Mallory), with the purpose of developing a framework and definition for microbiome stewardship, guiding principles for its implementation, and tools for assessment. We hope this could serve as a starting point for developing public policy around conservation of natural and built environments in ways that promote long-term health of everyone – people, plants, animals, microbes, and the planet.

What is “Microbiome Stewardship”?

Microbiome stewardship is the broad idea that we need to consider ecosystem-level factors when we think about public health, as our environment, behaviors, and public policy affects interactions between microbes and human health. Microbiomes are highly dynamic systems, featuring bacteria, archaea, protozoa, fungi, and viruses; and our personal microbiomes are derived from a larger shared, collective microbial resource. 

Figure from Robinson et al. 2022, mSystems

The importance of the human microbiome (the bacteria, fungi, archaea, protozoa, and viruses that we directly and indirectly interact with throughout our lives) for health and well-being has been well established. However, despite their demonstrated impact, there is limited information on the interconnectivity of non-host habitats (e.g., the built environment or other less intensively managed environments) and their collective contributions to human health. This includes interactions across scales such as with others in shared spaces, cultural and dietary practices, food systems and industrialized food processes, natural environments, built environments, and air pollution. 

The concept of the collective microbiome reinforces the idea of microbiomes as a public good from which all humans, plants, and animals derive benefit. Deterioration of the collective microbiome, and the increasing prevalence of microbiome dysbiosis in humans and elsewhere, is the least well-understood but the most-important facet of biodiversity loss and ecosystem health decline. Microbiome stewardship recognizes the necessity of microbial communities in sustaining human health, and emphasizes the imperative to protect them through policy and other action. Recognizing the importance of microbiome stewardship is a critical step, but we also lack the clear articulation needed to guide its implementation in policy and practice. We need a broadly applicable and inclusive definition of microbiome stewardship, a framework that can guide principles for implementation, and tools to assess microbiome health and to support informed decision making. 

Meet the Team

Dr. Kieran C. O’Doherty, PhD., is professor in the department of psychology at the University of Guelph, where he directs the Discourse, Science, Publics research Group. His research focuses on the social and ethical implications of science and technology and public engagement on science and technology. He has published on such topics as data governance, vaccines, human tissue biobanks, the human microbiome, salmon genomics, and genetic testing. A particular emphasis of his research is on theory and methods of public deliberation, in which members of the public are involved in collectively developing recommendations for the governance of science & technology. Recent edited volumes include Psychological Studies of Science and Technology (2019) and The Sage Handbook of Applied Social Psychology (2019). He is editor of Theory & Psychology.

Dr. Rob Beiko, PhD., is a Professor and Head of the Algorithms and Bioinformatics research cluster in the Faculty of Computer Science at Dalhousie University. His research aims to understand microbial diversity and evolution using machine learning, phylogenetics, time-series algorithms, and visualization techniques. His group is developing software tools and pipelines to comprehensively survey genes and mobile genetic elements in bacterial genomes, and understand how these genomes have been shaped by vertical inheritance, recombination, and lateral gene transfer. He is also a co-founder of Dartmouth Ocean Technologies, Inc., a developer of environmental DNA sampling devices.

Dr. Sue Ishaq, PhD., is an Assistant Professor of Animal and Veterinary Sciences, University of Maine; and founded MSE in 2020.  Over the years, her research has gone from wild animal gut microbiomes, to soils, to buildings, and back to the gut. Since 2019, her lab in Maine focuses on host-associated microbial communities in animals and humans, and in particular, how host and microbes interact in the gut and can be harnessed to reduce inflammation. She is also the early-career At-Large member of the Board of Directors for the American Society for Microbiology, 2024 – 2027. 

Emma AllenVercoe, PhD, is a Professor of Microbiology at the University of Guelph, and a Tier 1 Canada Research Chair in Human Gut Microbiome Function and Host Interactions. Her research portfolio is broad, encompassing host-pathogen interplay, live microbial products as therapeutic agents, gut microbiome and anaerobic culture (humans and animals), and the study of ‘missing gut microbes’ i.e. those that are present in hunter-gatherer societies but missing in the industrialized world.  She has developed the Robogut – a culture system that allows for the growth of gut microbial communities in vitro, and is currently busy with a centre for microbiome culture and preservation at the University of Guelph.

Dr. Mallory Choudoir, PhD, is an Assistant Professor & Soil Microbiome Extension Specialist in the Department of Plant & Microbial Biology at North Carolina State University. The goal of her applied research and extension program is to translate microbiome science to sustainable agriculture. She aims to develop microbial-centered solutions for optimizing crop productivity, reducing agronomic inputs, and enhancing  agroecosystem resilience to climate change.

Diego Silva, PhD, is a Senior Lecturer in Bioethics at Sydney Health Ethics and the University of Sydney School of Public Health. His research centers on public health ethics, particularly the application of political theory in the context of infectious diseases and health security, e.g., tuberculosis, COVID-19, antimicrobial resistance, etc. He is currently the outgoing Chair and a member of the Public Health Ethics Consultative Group at the Public Health Agency of Canada and works with the World Health Organization on various public health ethics topics on an ad hoc basis.

“Articulating Microbiome Stewardship: Definition, Guiding Principles, Framework”

Principal Investigator: Kieran O’Doherty, University of Guelph

co-Principal Investigators: Rob Beiko, Dalhousie University; Suzanne Ishaq, University of Maine. 

co-Investigators: Emma Allen-Vercoe, University of Guelph; Mallory Choudoir, North Carolina State University; Diego Silva, The University of Sydney School of Public Health.

Funding agency: Canadian Institute for Health Research

Abstract

The human microbiome is essential for healthy human development and immunity, and maintaining its health is a collective activity. In Canada and worldwide, there is an increasing prevalence of chronic illnesses attributed to dysbiosis of human microbiomes. The causes for microbiome dysbiosis vary. In part, the constitution of the human microbiome depends on genetic factors and personal lifestyle choices, such as diet and exercise. To a large extent, however, individuals’ and collective microbiomes are shaped by environmental factors including natural environments, built environments, food systems, air and other pollutants, and the microbiomes of other people and animals around us. Microbes, by their nature, are shared across humans, and between humans and the environments in which we live. Although our decisions as individuals may have some impact, it is mainly our actions as a society that shape macro-social influences such as environmental pollution, industrial food production, and guidelines for anti-biotic use, all of which profoundly affect human microbiomes. This suggests that we need a collective vision or principles that would act to coordinate and guide societal efforts to ensure healthy microbiome environments. In 2014 an interdisciplinary group of scholars proposed the concept of microbiome stewardship to recognise our shared microbial environment as a common good that needs to be protected. Although this was an important first step, the notion of microbiome stewardship needs to be developed in much more detail to be useful in guiding policy and practice. The purpose of this project is to develop an authoritative definition of microbiome stewardship, to develop guiding principles for its implementation, and to develop a framework for its assessment. We will use a series of interviews, workshops, and deliberative processes to engage a wide range of experts and stakeholders to develop a sustainable and comprehensive articulation of microbiome stewardship.