Ethical dimensions of microbiome research

A special MVIF event, with talks and panel discussion by:

Shani Msafiri Mangola, mutual aid organization Olanakwe, Tanzania
Dr. Alyssa Crittenden, University of Nevada, Las Vegas, USA
Katherine Amato, Northwestern University, USA
Pascale Vonaesch, University of Lausanne, Switzerland
Wim van Daele, Universitetet i Agder, Norway

The discussion will be chaired by Roberta Raffaetà - University Cà Foscari Venice, Italy, at the Atlantic event, and by Ugbad Farah - UC San Diego, USA, at the Pacific meeting.

Abstracts and speakers’ bios are available below.

Panel talks

For more information on the speakers, please read the “About the speakers” section below.

Ethics of microbiome research with Indigenous populations: the case of the Hadzabe community.

by Mr. Shani Msafiri Mangola, Director of Olanakwe Community Fund, Tanzania; Dr. Alyssa Crittenden, Professor of Anthropology and Human Biology, University of Nevada, Las Vegas, USA

With clinical applications of microbiome research now feasible, it is imperative that the science conducted, particularly among Indigenous communities, adheres to principles of inclusion and is community-based. This entails shared decision making on how biological samples are collected and who benefits from research and any derived products. Here, we share experiences from our own research endeavors with views from our own vantage points, one as an Indigenous human rights attorney and anthropological research assistant (Mangola) and one as a long time researcher with a key participant community in the microbiome research space (Crittenden). We introduce our approach that entails promising practices to carry out more ethical microbiome research with Indigenous communities.

Healthy collaboration: sharing the benefits and considering the consequences.

by Dr. Katherine Amato, Associate Professor and Microbiome Researcher at Northwestern University, USA

In this talk, I will explore how microbiome research benefits from collaboration across researchers and between researchers and communities. I will also discuss the challenges these relationships create in terms of credit, data access, and perceived versus actual knowledge benefits. While global collaborations are essential for addressing big scientific questions, they also run the risk of creating extractive practices at multiple levels.

Ethical considerations of research on the microbiome of vulnerable populations

by Dr. Pascale Vonaesch, Assistant Professor and Microbiome Researcher at the University of Lausanne, Switzerland

Today, microbiome knowledge and research is largely restricted to high- and middle-income countries, especially in North America, Europe as well as Asia. As the microbiome varies across geographies and lifestyles, it is of utmost importance to fill these “white gaps” and include also with communities and age groups that did not participate in these efforts to date. Many of these communities are- for different reasons- considered as vulnerable populations and including them in microbiome research thus poses many important ethical questions. In this presentation, I aim to give examples of ethical questions and constraints that arise when working on the microbiome of vulnerable populations. Giving examples from our research on the microbiome of undernourished children and their families from the Global South over the last years, I aim to stimulate discussion and reflection on these questions, to foster even better and more inclusive collaborations across cultures, disciplines and social structures in the future.

Ethical and rigorous human microbiome science requires radical interdisciplinary co-laboration.

by Dr. Wim van Daele, Associate Professor and Socio-Cultural Anthropologist at the Universitetet i Agder, Norway

Current human microbiome science is still marked by a European and North American bias with many important ethical implications on the horizon. In addition, the limited research on other understudied populations is not without its ethical quandaries either. In this presentation, I discuss and clarify these ethical issues by disentangling these into 3 main subsets: European and North American bias, cultural insensitivity, and lack of meaningful collaboration and inclusion. Thereafter, I propose an overall approach to solving these quandaries by introducing the notion of radical interdisciplinary co-laboration, in which different academic and non-academic stakeholders mediate their knowledges and labor together in studying human microbiomes. I will elicit how the proposed approach will render microbiome science more ethical and at the same time render the very science of microbiomes more precise and rigorous.

About the speakers (in presentation order)

Mr. Shani Msafiri Mangola

I am a member of the Hadza (Hadzabe) community of hunter-gatherers in Tanzania, East Africa. I am an Indigenous activist, a college graduate (Tumaini University Makumira, Tanzania), a holder of a Master of Law degree in Indigenous Peoples Law and Policy (from the University of Arizona, Tucson, USA), and an anthropology and human biology research assistant and collaborator. I am also the director of a mutual aid organization, Olanakwe Community Fund (https://www.olanakwe.org/), advocating for the equitable education of Hadzabe children who want to attend school in Tanzania. My motivation to engage in bioethics work comes from the belief that all public conversations about hunter-gatherers must be grounded in an understanding of the relationship between the community under study and the nation state.

Dr. Alyssa Crittenden

I am a Professor of Anthropology and Human Biology at the University of Nevada, Las Vegas. I come to this work as a non-Indigenous woman who is descended from European and Mexican immigrants. I have expertise and training in nutrition, ecology, human biology, and anthropology. I have worked with the Hadzabe community of hunter-gatherers in Tanzania for twenty years, largely focused on diet composition and reproduction.

Dr. Katherine Amato

Dr. Amato is a biological anthropologist at Northwestern University studying the influence of gut microbes on host ecology and evolution. Her research examines how diet affects the gut microbiota as well as how changes in the gut microbiota impact host nutrition, energetics, and health. She uses non-human primates as models for studying host-gut microbe interactions in selective environments and for providing comparative insight into the evolution of the human gut microbiota. Her main foci are understanding how the gut microbiome may buffer hosts during periods of nutritional stress and how the gut microbiome programs normal inter-specific differences in host metabolism. In this realm, she is also interested in global variation in the human gut microbiome and its implications for local human adaptation. Dr. Amato obtained her A.B. in Biology from Dartmouth College and her Ph.D. in Ecology, Evolution and Conservation Biology from the University of Illinois at Urbana-Champaign. She completed a postdoc at the University of Colorado Boulder. She is now an Associate Professor in the Department of Anthropology at Northwestern University. She is also affiliated with the Interdisciplinary Biological Sciences Graduate Program and sits on the Executive Committee of the Northwestern Institute on Complex Systems. Dr. Amato is the President of the Midwest Primate Interest Group, an Associate Editor at Microbiome, an Editorial Board member at Folia Primatologica, and a Fellow for the Canadian Institute of Advanced Research’s ‘Humans and the Microbiome’ Program.

Dr. Pascale Vonaesch

Pascale Vonaesch, MSc, MPH, PhD is an Assistant Professor at the University of Lausanne and a Principal Investigator within the NCCR Microbiomes. She was trained as a Microbiologist at the ETH in Zürich and the Ecole Normale Supérieure in Paris and subsequently performed her PhD thesis at the Institut of Microbiology at the ETH in Zürich, Switzerland on host-pathogen interactions and a postdoctoral research stay at the Institut Pasteur, Paris, France, where she initiated and led the Afribiota project, a translational research project aimed at elucidating the pathophysiology underlying stunted child growth. She then joined the Swiss Tropical and Public Health Institute for two years as a senior postdoc/ junior group leader to continue her work on undernutrition before moving with her group to the University of Lausanne. Her lab focuses on fundamental and translational/clinical research on the human intestinal ecosystem and the contribution of the microbiota to health and disease. In her research, she is especially interested in the role of the intestinal microbiome in childhood malnutrition and in the development of microbiota-targeted interventions. For her projects, she works since more than fifteen years in close collaboration with colleagues from the Global South, mainly in Africa and Laos.

Dr. Wim van Daele

Wim Van Daele has a PhD in comparative science of cultures and Interdisciplinary Studies from the Vrije Universiteit Brussel and Ghent University in Belgium and is specialized in the anthropology of food and food systems. His PhD and postdoctoral research at the University of Oslo drew upon the anthropology of food and medical anthropology studying the relationships between food and society and health in Sri Lanka. He was also a visiting researcher at the Food Studies Centre at the School of Oriental and African Studies at the University of London, the University of Chicago and Columbia University. Gradually, he has turned his focus toward epigenetics and microbiomics as part of his program to elicit the intersections between (micro)biological and socio-cultural processes shaping locally situated human biologies. In 2021, he became an associate professor in the Department of Nutrition and Public Health at the University of Agder in Norway, where he currently leads the large interdisciplinary EATWELL project on food in Bhutan, examining the socio-cultural, nutritional and environmental aspects of food systems across different sites. He is currently establishing a collaboration with the Raes Lab in Belgium to integrate a significant microbiome part into the EATWELL project, enabling the study of how society and environment enter into the gut via food systems and eating.

Short Talks

Expanding the human gut microbiome atlas of Africa

Population studies are crucial in understanding the complex interplay between the gut microbiome and geographical, lifestyle, genetic, and environmental factors. However, populations from low- and middle-income countries, which represent ∼84% of the world population, have been excluded from large-scale gut microbiome research. Here, we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,803 women from Burkina Faso, Ghana, Kenya, and South Africa. By intensively engaging with communities that range from rural and horticultural to urban informal settlements and post-industrial, we capture population diversity that represents a far greater breadth of the world’s population. Using shotgun metagenomic sequencing, we find that study site explains substantially more microbial variation than disease status. We identify taxa with strong geographic and lifestyle associations, including loss of Treponema and Cryptobacteroides species and gain of Bifidobacterium species in urban populations. We uncover a wealth of prokaryotic and viral novelty, including 1,005 new bacterial metagenome-assembled genomes, and identify phylogeography signatures in Treponema succinifaciens. Finally, we find a microbiome signature of HIV infection that is defined by several taxa not previously associated with HIV, including Dysosmobacter welbionis and Enterocloster sp. This study represents the largest population-representative survey of gut metagenomes of African individuals to date, and paired with extensive clinical biomarkers, demographic data, and lifestyle information, provides extensive opportunity for microbiome-related discovery and research.

Link to preprint: https://www.biorxiv.org/content/10.1101/2024.03.13.584859v1

Dylan Maghini, Department of Medicine, Stanford University, Stanford, CA, USA & Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa

The Leke Project: raise awareness on vaginal health in Cameroon

Research on vaginal microbiome is expanding worldwide. Increasingly, research is being directed towards remote countries or communities where microbiome data were previously non-existent, and this is sometimes accompanied by challenges in communication, recruiting participants, collecting samples, and even transporting and storing these samples. The Leke project is an Isala sister project carried out in Cameroon which aims to map the vaginal microbiome of healthy women and break the taboo around vaginal health. Particularly in the Leke project, we raised awareness about vaginal health and healthy practices in remote communities by including in the conversation to men and women. In this presentation, we will explain the challenges we faced and how we overcame them to research the vaginal microbiome.

Link to Josiane’s blog about the project: https://isala.be/en/the-leke-project-a-journey-to-the-isala-sister-project-in-cameroon/

Josiane Kenfack, University of Yaounde I, Cameroon, & University of Antwerp, Belgium