Last week in Guelph, Ontario, Canada, I had the unique please of “nerding out” with long-time colleagues (who I was meeting in-person for the first time) about microbial ecology questions that we wanted to answer, the science fiction we were reading, which metal band to listen to for the winter holidays, how to perform large-scale research on a tight budget, and whether the next season of whatever show had piqued our interest would be any good. The nerds-in-question are the Microbiome Stewardship research group, led by the intrepid Kieran O’Doherty, that I’ve been a part of for the past few years (and longer, counting the time we’ve collaborated through the Microbes and Social Equity working group).
Left to right; front: Zhongzhi (Michael) Sun, Emma Allen-Vercoe, Sue Ishaq; middle: Mikaela Beijbom, Mallory Choudoir, Sarah Elton, Kieran O’Doherty, Panuya Athithan; back: Grace Gabber, Andreas Heyland, Rob Beiko.
Over two days, my microbiome stewardship colleagues and I (both original team and expansion pack researchers) shaped our concept of what it means to share microbes between individuals, communities, and ecosystems; what it would mean to consider microbes as a natural resources to which everyone had an innate right to; and how it would look for public and planetary health to reduce the harm of human industry and consumerism to live more sustainably and regain all the benefits that the microbial world can provide us. Our of this meeting, we imagined what the focus of our next year or two of research will look like, as individual researchers and as a group, as we embark on the next phase of our multi-year project: case studies of how microbiome stewardship could be tailored, implemented, and evaluated. These studies will be published as they are completed and pass peer review, in a scientific journal online (announcement forthcoming).
This research ideation meeting followed two years of conversation, presentations, a symposium (sessions can be viewed here), journal articles, and a whole lot of research-, personnel-, and travel-coordination on the part of our research wrangler, Mikaela Beijbom, who has been helping us to organize our words and activities for the past 8 months.
As this tumultuous and combative year comes to a close, and as I prepare to end the “break” which was my semester-long sabbatical and return to 50-hour work weeks, the precious opportunity to let our minds wander – through work, life, and play – was a brief return to the pure joy of scientific discovery which drew us all to our careers. This year, scientists have faced hurdle after hurdle placed by the very public research institutions which were created to help us seek knowledge on behalf of the public good. Funding cuts have reduced the scientific workforce; lost precious time, expertise, and data; and disrupted the innovation and ideation process which research forges. Yet, the time I spent with colleagues last week was a reminder that knowledge generation, public good, scientific inquiry, and collaboration are values which cannot be defunded, banned, or curtailed so easily. As for our group, we’ll keep meeting (virtually, at least) throughout 2026 and beyond, for the love of science.
Our collaborative team of researchers (bioethicists (Kieran and Diego), bioinformaticians (Rob), host microbial ecologists (Sue and Emma), and soil microbial ecologists (Mallory), had our first co-authored paper published in mSystems! Our paper is a commentary on the concept and need for microbiome stewardship, and outlines the research and policy priorities that are the focus of our ongoing research.
Microbiome scientists are increasingly demonstrating the importance of microbial ecologies for human and environmental health. In spite of this, no protections are in place to ensure the health of microbiomes. In other words, there are no policies protecting microbiomes, which in turn are foundational to the health of all environmental and host ecosystems. We built our research team to develop a framework and definition for microbiome stewardship, guiding principles for its implementation, and tools for assessment. Last year, we were awarded funding from the Canadian Institutes for Health Research (CIHR) for a four-year project investigating how our collective microbiomes (the diverse microbes we share between humans and our environments) impact health! The publication of this commentary also sets the stage for a Summit on Pathways to Microbiome Stewardship which the research team is organizing for July 7-10, 2025.
Abstract: Microbiomes are essential for human, animal, plant, and ecosystem health. Despite widespread recognition of the importance of microbiomes, there is little attention paid to monitoring and safeguarding microbial ecologies on policy levels. We observe that microbiomes are deteriorating owing to practices at societal levels such as pesticide use in agriculture, air and water pollution, and overuse of antibiotics. Potential policy on these issues would cross multiple domains such as public health, environmental protection, and agriculture. We propose microbiome stewardship as a foundational concept that can act across policy domains to facilitate healthy microbiomes for human and ecosystem health. We examine challenges to be addressed and steps to take toward developing meaningful microbiome stewardship.
Figure 1. Microbiome stewardship as a concept and framework for ensuring human and planetary health supported by microbial functions. Human microbiomes are constituted from our environment, which has determinants based largely on societal systems (e.g., agriculture and food systems, built environment, health care accessibility) that operate beyond individual choice and behavioral interventions. Figure created with BioRender.com.
Acknowledgments: We thank Lola Holcomb for their helpful feedback and organizational contributions to this manuscript.
Funding: United States Department of Agriculture National Institute of Food and Agriculture Hatch Project Accession 7004439 (MJC) United States Department of Agriculture National Institute of Food and Agriculture through the Maine Agricultural & Forest Experiment Station: Hatch Project ME022329 (SLI) National Institute of Health (NIH/NIDDK 1R15DK133826-01) (SLI) Canadian Natural Sciences and Engineering Research Council (RGB) Canada Research Chairs program (EA-V) Canadian Institutes of Health Research (Funding Reference Number: 191753) (KCO) University of Guelph Institute for Environmental Research (KCO)
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 Associate Professor of Microbiomes, 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.
Dr. 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 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.
Our 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!
We are seeking a suitable candidate for a post-doctoral fellowship to work on the concept of microbiome stewardship. This is a unique interdisciplinary opportunity to develop skills and a research profile across natural sciences, social sciences, and humanities scholarship. Microbiome stewardship is a new concept that combines:
knowledge from microbiology about the importance of microbiomes for health and development of humans, other animals, and plants;
knowledge from bioethics about the importance of developing ethical guidance and policy to ensure the health of humans and others;
knowledge from the social sciences about public and stakeholder engagement to develop principles for microbiome stewardship that are informed by a broad set of perspectives and areas of expertise;
recognition of the environmental determinants of health of microbiomes of organisms.
We require a highly accomplished individual to assist in developing a guiding framework for microbiome stewardship. This will involve conceptual work, networking with microbiome and other scientists, and strong project management skills.
Required skills for the position include: project management; high standard of writing. Preferred (not required) skills include: microbiology/microbiome science; social science methods (interviewing; focus groups); experience with policy.
Successful candidate should have a PhD in a discipline relevant to the needs of the project (e.g., public health; environmental science; microbiology; human geography; science & technology studies). It is not necessary that the candidate has expertise in all aspects of the project. For the initial phases of the project, we will favour applicants with expertise in the social sciences, policy development, or public health. However, individuals with expertise in other fields (for example, microbiology) are also encouraged to apply if they can demonstrate skills or experience in translating their knowledge into policy.
Location: Ideally, the position will be based at the University of Guelph (Canada); however, it is also possible to work from one of the other project sites in Canada or the USA (University of Maine; Dalhousie University; North Carolina State University). The position is supported by funding from the Canadian Institutes of Health Research.
Starting date: negotiable with possibility to start immediately
Salary: dependent on candidate skill and experience
To apply, send an email to Kieran O’Doherty at odohertk@uoguelph.ca indicating your interest in the position. Please include a cv or resume; academic transcripts; publications or other writing samples (e.g., course papers; policy documents; research reports).
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.
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.
About the research 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.
Dr. 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 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.
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 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.
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.
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.
Dr. 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 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.
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 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.
The Ishaq Lab 