An ethical way forward for Indigenous microbiome research
Science has a history of exploitation and extraction. Microbiologists have the chance to take a different approach. By Sam Jones
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“I’m tired of giving parts of my body away.”
When anthropologist Alyssa Crittenden heard these words ten years ago, she knew that she needed to make a change.
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A decade earlier, in 2004, she was a doctoral student investigating the connection between diet and reproduction. Her work led her to the Hadza people — a group of Indigenous hunter-gatherers in Tanzania with a diet and lifestyle that are very different from those of people in the United States and other industrialized societies.
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Anthropologist Alyssa Crittenden (right) has worked with the Hadza community in Tanzania for 20 years. Credit: Alyssa Crittenden
The Hadza’s lifestyle is reflected in the bacteria and other microorganisms that live inside their guts. Every human is home to trillions of microbes, known collectively as the microbiome. As the availability of genetic and data-analysis tools has increased, the microbiome has been implicated in countless diseases, including cancer, diabetes and inflammatory bowel disease.
Through the work of several researchers, including Crittenden — who is at the University of Nevada, Las Vegas — it has also become clear that the diversity of microbes in the guts of people living in Indigenous communities is typically greater than that in the guts of people living in industrialized societies. This finding, and the concern that reduced microbial diversity owing to the consumption of processed foods and antibiotics might make people in industrialized societies more vulnerable to some chronic diseases, has fuelled interest in the idea of restoring the gut to a more ancestral, pre-industrialized state.
In the early 2010s, Crittenden was working with a multi-university team on a gut-microbiome project with the Hadza. They were not the only researchers interested — Crittenden remembers researchers from around the globe flocking to study the Hadza. She was particularly interested in investigating the microbial make-ups that allowed the Hadza to digest and extract nutrition from the staple wild foods in their diets, including various tubers composed of tough, insoluble fibres. “It’s like chewing on the most fibrous piece of celery you’ve ever had,” she says.
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Wild tubers are a staple component of the Hadza people’s diet. Credit: Federico Neri/Pacific Press/Shutterstock
The team analysed faecal samples from the Hadza and, in 2014, its work was the first paper published on the gut microbiome of a foraging population1. The seminal work showed that compared with people in Western urban areas, the Hadza had increased gut microbial diversity, as well as higher levels of certain microbes that the researchers suggested could help the Hadza to digest fibre-rich foods.
But Crittenden no longer collects biological samples from the Hadza.
![Four women in conversation and sitting on the ground outside. Three are members of the Hadza community; they appear happy. The other woman, sat slightly behind the group, is Alyssa Crittenden. She is holding a notebook and pen and taking notes.](./assets/Kpsf4AuKoj/02_alyssa-interviewing-3718x3724.jpg)
Anthropologist Alyssa Crittenden (right) has worked with the Hadza community in Tanzania for 20 years. Credit: Alyssa Crittenden
Anthropologist Alyssa Crittenden (right) has worked with the Hadza community in Tanzania for 20 years. Credit: Alyssa Crittenden
![The hand of a Hadza man picking honey out of a cut tree trunk](./assets/GyH8ofe84M/shutterstock_1508543330-4096x2634.jpg)
Honey is an important food for Hadza hunter-gatherers. Credit: Katiekk/Shutterstock
Honey is an important food for Hadza hunter-gatherers. Credit: Katiekk/Shutterstock
![Hadza girls digging in the ground for buried tubers using a pointed stick](./assets/uBl288yP0k/shutterstock_editorial_11841652aj-4096x2731.jpg)
Wild tubers are a staple component of the Hadza people’s diet. Credit: Federico Neri/Pacific Press/Shutterstock
Wild tubers are a staple component of the Hadza people’s diet. Credit: Federico Neri/Pacific Press/Shutterstock
Around the time the study was published, Crittenden found herself sitting with a Hadza friend on a blanket under the shade of a large baobab tree, the woman’s granddaughter playing at their feet.
“She said, ‘I’m tired of giving parts of my body away.’” Crittenden recalls. “‘We’re tired, we’re exhausted, and we’re not really getting much out of all of this research.’”
Crittenden will never forget that moment, and feeling the weight of how the never-ending requests for samples of faeces, hair, breast milk and more from so many research teams was affecting her friend. “That was the point where I said ‘from here on out, I’m going to do things differently’,” she says.
At the time, Crittenden was already working on another project with the Hadza, comparing the effects of wild and processed foods on dental health. She and her colleagues immediately began updating the research protocols to make them less invasive, for example by replacing physical dental examinations with imaging.
The more thought she and her colleagues put into the ethics of their work, and the more they learnt about the treatment of Indigenous communities by scientists throughout history, the more Crittenden realized that her friend’s concerns were just the tip of the iceberg. “My eyes were opened initially in that moment, but they continued to open wider and wider,” Crittenden says.
“It would be disingenuous if I didn’t acknowledge my own role that I had played in this, and that my own career had been built on collecting samples, and indeed taking part of my research participants’ bodies.”
![A baobab tree. It has no leaves.](./assets/GOMi58KN5z/nature_tanzani_46-4096x2732.jpg)
For centuries, Indigenous communities have experienced the theft of their lands, their ancestors’ remains and, more recently, the unethical collection and use of their DNA without consent. “What we have seen is just an egregious abuse of power, an egregious culture of extraction,” says geneticist Keolu Fox, who is Kānaka Maoli (Native Hawaiian) and co-founder of the Indigenous Futures Institute at the University of California, San Diego.
Some Indigenous and non-Indigenous researchers are now working to draw up ethical frameworks for microbiome research with Indigenous communities. However, the rapid growth of the field has so far outpaced the formation of national or international agreements on the ethical collection, storage or use of microbiome data from Indigenous people, or on compensation for the people who provide them. “How rapidly we can sequence something and create data and commodify it — I don’t think that the policy has caught up,” says Fox.
He and many other researchers think that there is an ethical way forward, and most say that it will require placing research decisions and data in the hands of Indigenous communities — as well as ensuring that the people who participate in research are able to reap the benefits that might come from it.
![A man in a smart shirt with a large necklace over the top, stood in front of a blue screen. He has a microphone and is gesturing as if making a point.](./assets/P9DIiHIk5r/24425842413_a90935cc59_o-1920x1280.jpg)
Geneticist Keolu Fox advocates for Indigenous people to be involved in research. Credit: Ryan Lash/TED
Geneticist Keolu Fox advocates for Indigenous people to be involved in research. Credit: Ryan Lash/TED
“We have seen an egregious abuse of power, an egregious culture of extraction.”
For centuries, Indigenous communities have experienced the theft of their lands, their ancestors’ remains and, more recently, the unethical collection and use of their DNA without consent. “What we have seen is just an egregious abuse of power, an egregious culture of extraction,” says geneticist Keolu Fox, who is Kānaka Maoli (Native Hawaiian) and co-founder of the Indigenous Futures Institute at the University of California, San Diego.
![A man in a smart shirt with a large necklace over the top, stood in front of a blue screen. He has a microphone and is gesturing as if making a point.](./assets/P9DIiHIk5r/24425842413_a90935cc59_o-1920x1280.jpg)
Geneticist Keolu Fox advocates for Indigenous people to be involved in research. Credit: Ryan Lash/TED
Geneticist Keolu Fox advocates for Indigenous people to be involved in research. Credit: Ryan Lash/TED
Some Indigenous and non-Indigenous researchers are now working to draw up ethical frameworks for microbiome research with Indigenous communities. However, the rapid growth of the field has so far outpaced the formation of national or international agreements on the ethical collection, storage or use of microbiome data from Indigenous people, or on compensation for the people who provide them. “How rapidly we can sequence something and create data and commodify it — I don’t think that the policy has caught up,” says Fox.
He and many other researchers think that there is an ethical way forward, and most say that it will require placing research decisions and data in the hands of Indigenous communities — as well as ensuring that the people who participate in research are able to reap the benefits that might come from it.
Learning by listening
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Crittenden says that she had only good intentions when she began working with the Hadza. “Most research scientists who I’ve known believe that the work they’re doing is valuable for the scientific community.” But therein lies the key tension — something that is valuable to the scientific community might not be valuable to the people who are providing the samples and might, in fact, interfere with their lives.
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The lifestyle of the Hadza people is very different from that of people in industrialized societies. Credit: Patrick Meinhardt/Panos Pictures for Nature
After the pivotal conversation with her Hadza friend, Crittenden’s next trip to Tanzania was to find out what community members were interested in learning about their health and environment. There were a huge number of requests. “I took the long list that I had and brought it back to the students and to my collaborators, and we thought long and hard about what we could do,” she says. “What is fundable? What is doable in the short term? What is doable in the long term?”
Since then, her work with the community has included studies on the influence of diet on growth during childhood2, and on how changes in health-care access and diet are affecting Hadza birth and perinatal care practices3. In 2020, Crittenden and Hadza community members created a non-profit organization called the Olanakwe Community Fund, which supports educational and economic-development projects that directly benefit the Hadza people.
“As a scientist, sometimes you need to take a back seat and listen to what the community is interested in identifying and addressing for their needs,” says Matthew Anderson, a microbiologist of Eastern Band of Cherokee Indians descent, at the University of Wisconsin–Madison.
![Three Hadza women walk in a line back to their camp](./assets/AWyKLtfmV1/nature_tanzani_31-1-4096x2732.jpg)
The lifestyle of the Hadza people is very different from that of people in industrialized societies. Credit: Patrick Meinhardt/Panos Pictures for Nature
The lifestyle of the Hadza people is very different from that of people in industrialized societies. Credit: Patrick Meinhardt/Panos Pictures for Nature
![A Hadza woman sits by a campfire, holding a small child inside her blanket.](./assets/OPmxnnTRZi/nature_tanzani_25-1-4096x2732.jpg)
Changes in diet can affect the growth of Hadza children. Credit: Patrick Meinhardt/Panos Pictures for Nature
Changes in diet can affect the growth of Hadza children. Credit: Patrick Meinhardt/Panos Pictures for Nature
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Much of Anderson’s work is done in collaboration with the Lakota people in South Dakota, whose incidence of rheumatoid arthritis — a chronic and painful autoimmune disease that affects the joints — is five times higher than the US average.
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Matthew Anderson is a microbiologist at the University of Wisconsin–Madison. Credit: The Ohio State University
Anderson first visited the Lakota people on the Cheyenne River reservation in 2011, as a postdoctoral researcher. He was asked to join existing projects owing to his microbiology expertise.
By 2018, most of those projects were wrapping up, but Lakota community members told Anderson there were still many questions they wanted answered — those related to rheumatoid arthritis, in particular. One of the early projects Anderson had been brought in on was focused on rheumatoid arthritis, but the way it operated “actually was pretty harmful”, he recalls. Some researchers, he says, had assumed that they knew better than the community and tried to forge ahead with their preferred plans regardless of approval from the Lakota people.
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Matthew Anderson (fourth from left) first visited the Cheyenne River reservation in South Dakota in 2011. Credit: Ḵaa Yahaayí Shkalneegi Muriel Reid
Anderson decided to instead engage with the Lakota, and soon found out that they were interested in understanding if their microbiomes were contributing to a higher incidence of the disease. Before securing funding, he shared with them what a project would entail and what tangible benefits there would be to the community. The work they agreed to undertake together continues today.
![A photo of the face and shoulders of Matthew Anderson. He is wearing a collared shirt and looking at the camera.](./assets/QSykLXbwX8/anderson_landscape-copy-874x492.jpg)
Matthew Anderson is a microbiologist at the University of Wisconsin–Madison. Credit: The Ohio State University
Matthew Anderson is a microbiologist at the University of Wisconsin–Madison. Credit: The Ohio State University
![A group of 9 people in t-shirts and jumpers stood around in a large field. The sky is blue with clouds, and there is only flat open grassland all the way to the horizon.](./assets/CgKL3kznpY/20220615-indigidata-murielreid-14-1-2-4096x2731.jpg)
Matthew Anderson (fourth from left) first visited the Cheyenne River reservation in South Dakota in 2011. Credit: Ḵaa Yahaayí Shkalneegi Muriel Reid
Matthew Anderson (fourth from left) first visited the Cheyenne River reservation in South Dakota in 2011. Credit: Ḵaa Yahaayí Shkalneegi Muriel Reid
Co-designing projects with Indigenous communities in this way might take more time, but it is essential to doing ethical research, says Aviaja Lyberth Hauptmann, a microbiologist at the University of Greenland in Nuuk.
In 2017, she launched the Greenland Diet Revolution project, and began investigating what microbes are involved in making a diversity of traditional animal-based foods popular in Inuit culture4, such as the fermented intestinal contents of animals including seals, sea birds, walruses, reindeer and musk oxen.
The project was, in part, a push-back against the promotion of fibre-rich, heavily plant-based diets as humanity’s shared ancestral lifestyle and the route to a healthy gut microbiome. As a member of the Inuit Arctic Indigenous community herself, this is not the ancestry Hauptmann recognizes.
“When I think about an ancestral diet, it’s not a forager diet,” she says. “It’s a hunter’s diet.”
![A vast expanse of snow and ice. In the far distance are the outlines of large mountains. In the foreground, but still far from the camera, there is a team of dogs, some sleds and a single person stood in the centre.](./assets/niAMzEHggn/06_greenlanddaniel_hauptmann_dh2-3008x2000.jpg)
Her desire to dispel this oversimplified view of Indigenous diets and microbiomes led her to northern Greenland, home to Inuit people known as Inughuit. “I had never been there before. I was not invited there. I just assumed access and I went,” Hauptmann recalls.
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Microbiologist Aviaja Lyberth Hauptmann has sampled seal intestines in northern Greenland. Credit: Carsten Egevang
Her initial trip to the region was to collect microbiome samples from community members, but it was during the following trip, while collecting samples of fermented foods, that she met a wonderful family, Hauptmann says, who informed her of her mistake.
The mother of the family had been angry that Hauptmann had just assumed she could show up and do research in their community. It was an eye-opening experience for Hauptmann.
“When you’re not an insider to a community, and you look at something from a position of scientific curiosity, there can be things that are very interesting and fascinating,” she says. “But if you’re in the community, it feels incredibly disrespectful.”
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Hauptmann intends to use samples from Inughuit people in Greenland to answer questions that matter to that community. Credit: Carsten Egevang
Hauptmann has yet to process those microbiome samples from Inughuit people, because she is still working with the community on exactly what questions they would like answered. “There’s this narrative of urgency around some of this research,” she says, which is fuelled by concerns that Indigenous communities are disappearing and taking their sought-after microbes with them. But for Hauptmann, taking the time to ensure the work she is doing will be relevant to the groups providing samples is an ethical necessity.
![The hands of Aviaja Hauptmann are seen cutting a sample of seal intestines with a scalpel. On one hand she has several fine-line tattoos that form bands around her palm and fingers.](./assets/s89QS2Ds7w/02_greenland_carsten_egevang_ce2-2000x1335.jpg)
Microbiologist Aviaja Lyberth Hauptmann has sampled seal intestines in northern Greenland. Credit: Carsten Egevang
Microbiologist Aviaja Lyberth Hauptmann has sampled seal intestines in northern Greenland. Credit: Carsten Egevang
![9 small sealed plastic tubes laid on a wooden surface. The tubs contain cotton buds coated in brown and red substances. Each tube has a hand-written code on the side.](./assets/9dpFgC2uHu/05_greenlandcarsten_egevang_ce5-2500x1668.jpg)
Hauptmann intends to use samples from Inughuit people in Greenland to answer questions that matter to that community. Credit: Carsten Egevang
Hauptmann intends to use samples from Inughuit people in Greenland to answer questions that matter to that community. Credit: Carsten Egevang
The greater good?
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The concern that the microbiomes of Indigenous people might not be around to study for much longer is a driving force behind the Microbiota Vault — a non-profit initiative founded in 2019 with the mission of preserving global microbial diversity, including the microbiomes of Indigenous people, to “conserve long-term health for humanity”.
“Within each country, there are likely to be teams of researchers and Indigenous peoples working together to collect these specimens and preserve them locally,” says Rob Knight, a microbiologist at the University of California, San Diego, and vice-president of the Microbiota Vault. The physical vault will keep back-up samples from local collections safe, “kind of like the seed bank in Svalbard”, Knight says, referencing the facility in the Arctic that stores more than one million seed samples from countries across the globe in an effort to secure the world’s food supply.
Samples held in the Microbiota Vault will only be accessible to the depositor. However, if depositors take up the organization’s offer of free sequencing of those samples, the terms require that the results be uploaded to an open-access database for anyone to use.
Fox is one of a number of researchers concerned that the Microbiota Vault is reminiscent of earlier efforts such as the Human Genome Diversity Project, which sought preferentially to collect biological samples such as blood and saliva from isolated populations at risk of disappearing to “study the genetic richness of the entire human species”. In 1993, the World Council of Indigenous Peoples dubbed it “the Vampire Project” owing to what it perceived as the use of Indigenous peoples’ genetic information for the benefit of others, with no consideration for the communities themselves.
For Fox, the Microbiota Vault’s goal of helping all of humanity is worryingly familiar. “The greater good argument is getting tired and old,” he says. “Whose greater good are we talking about here?”
Microbiota Vault president Maria Gloria Dominguez-Bello, a microbiologist at Rutgers University in New Brunswick, New Jersey, acknowledges that there has been “a history of exploitation and abuses and immorality” towards Indigenous peoples. However, she does not think that their samples should be excluded from the Microbiota Vault or from any other ethically conducted study that is aimed at improving human health. “I don’t think it’s ethical to exclude any human population,” she says.
![A photograph of Rob Knight smiling in the lobby of a large building](./assets/E4vwptVPk2/knight-rob-lobby1_credit-kyle-dykes-ucsd-oct-2019-1080x720.jpg)
Microbiologist Rob Knight is the vice-president of the Microbiota Vault. Credit: Kyle Dykes/UCSD
Microbiologist Rob Knight is the vice-president of the Microbiota Vault. Credit: Kyle Dykes/UCSD
“Whose greater good are we talking about here?”
The concern that the microbiomes of Indigenous people might not be around to study for much longer is a driving force behind the Microbiota Vault — a non-profit initiative founded in 2019 with the mission of preserving global microbial diversity, including the microbiomes of Indigenous people, to “conserve long-term health for humanity”.
“Within each country, there are likely to be teams of researchers and Indigenous peoples working together to collect these specimens and preserve them locally,” says Rob Knight, a microbiologist at the University of California, San Diego, and vice-president of the Microbiota Vault. The physical vault will keep back-up samples from local collections safe, “kind of like the seed bank in Svalbard”, Knight says, referencing the facility in the Arctic that stores more than one million seed samples from countries across the globe in an effort to secure the world’s food supply.
![A photograph of Rob Knight smiling in the lobby of a large building](./assets/E4vwptVPk2/knight-rob-lobby1_credit-kyle-dykes-ucsd-oct-2019-1080x720.jpg)
Microbiologist Rob Knight is the vice-president of the Microbiota Vault. Credit: Kyle Dykes/UCSD
Microbiologist Rob Knight is the vice-president of the Microbiota Vault. Credit: Kyle Dykes/UCSD
Samples held in the Microbiota Vault will only be accessible to the depositor. However, if depositors take up the organization’s offer of free sequencing of those samples, the terms require that the results be uploaded to an open-access database for anyone to use.
Fox is one of a number of researchers concerned that the Microbiota Vault is reminiscent of earlier efforts such as the Human Genome Diversity Project, which sought preferentially to collect biological samples such as blood and saliva from isolated populations at risk of disappearing to “study the genetic richness of the entire human species”. In 1993, the World Council of Indigenous Peoples dubbed it “the Vampire Project” owing to what it perceived as the use of Indigenous peoples’ genetic information for the benefit of others, with no consideration for the communities themselves.
“Whose greater good are we talking about here?”
For Fox, the Microbiota Vault’s goal of helping all of humanity is worryingly familiar. “The greater good argument is getting tired and old,” he says. “Whose greater good are we talking about here?”
Microbiota Vault president Maria Gloria Dominguez-Bello, a microbiologist at Rutgers University in New Brunswick, New Jersey, acknowledges that there has been “a history of exploitation and abuses and immorality” towards Indigenous peoples. However, she does not think that their samples should be excluded from the Microbiota Vault or from any other ethically conducted study that is aimed at improving human health. “I don’t think it’s ethical to exclude any human population,” she says.
![](./assets/D3Vtk0SiHT/carry-animation-final-frame-0ms-1920x1080.jpg)
The Microbiota Vault is still in its pilot phase, with various regions of the world being scouted to serve as its location. At the same time, says Knight, the team is evaluating the ethical models that it hopes to put in place before samples are deposited, including ensuring that researchers comply with religious and community expectations for interacting with participants and allowing providers of biological samples to retain control over those specimens. It is also discussing whether and how profits from any supplements or drugs that might be developed off the back of this research will be allocated. “We’re trying to avoid all of those categories of mistakes up front,” he says.
Ensuring that Indigenous communities benefit from their involvement in research is essential. The alternative is “biological theft,” says Crittenden — “going in and extracting biological materials from communities and profiteering off of those without any compensation back to the community.”
But the field’s current data-sharing structure makes this a challenge. Once a person’s microbiome data are uploaded to a public database, they are fair game. “You can’t prevent it from being used to make some sort of discovery that’s valuable,” says Knight.
If and when those data are used to develop microbiome-based therapeutics, the companies that are looking to sell the product typically won’t think of the Indigenous communities that made it possible, says Krystal Tsosie, an Indigenous geneticist and bioethicist at Arizona State University in Tempe. There is typically little thought to providing either financial compensation or access to the drugs to these communities. “They want to reintroduce a healthy or pre-industrial microbiome, into, frankly, wealthy patients who can afford these technologies,” she says.
“We’re trying to avoid all of those categories of mistakes upfront."
The Microbiota Vault is still in its pilot phase, with various regions of the world being scouted to serve as its location. At the same time, says Knight, the team is evaluating the ethical models that it hopes to put in place before samples are deposited, including ensuring that researchers comply with religious and community expectations for interacting with participants and allowing providers of biological samples to retain control over those specimens. It is also discussing whether and how profits from any supplements or drugs that might be developed off the back of this research will be allocated. “We’re trying to avoid all of those categories of mistakes up front,” he says.
Ensuring that Indigenous communities benefit from their involvement in research is essential. The alternative is “biological theft,” says Crittenden — “going in and extracting biological materials from communities and profiteering off of those without any compensation back to the community.”
“We’re trying to avoid all of those categories of mistakes upfront."
But the field’s current data-sharing structure makes this a challenge. Once a person’s microbiome data are uploaded to a public database, they are fair game. “You can’t prevent it from being used to make some sort of discovery that’s valuable,” says Knight.
If and when those data are used to develop microbiome-based therapeutics, the companies that are looking to sell the product typically won’t think of the Indigenous communities that made it possible, says Krystal Tsosie, an Indigenous geneticist and bioethicist at Arizona State University in Tempe. There is typically little thought to providing either financial compensation or access to the drugs to these communities. “They want to reintroduce a healthy or pre-industrial microbiome, into, frankly, wealthy patients who can afford these technologies,” she says.
Concerns about unethical collection, storage and use of Indigenous data were a big motivator for the formation of the Native BioData Consortium. Founded in 2018, it is the first non-profit research institute in the United States run by Indigenous scientists and community members.
The group manages a biobank located on sovereign Native American land in Eagle Butte, South Dakota. The consortium stores a variety of biological and non-biological samples and data in partnership with collaborating Native American communities. “Having the biobank on sovereign Native land, where tribal laws and resolutions are in place, can afford additional protection for Indigenous communities who wish to engage in biomedical and other types of research,” says Tsosie, who is a co-founder and board member of the consortium. Fox and Anderson are also board members.
Unlike at the Microbiota Vault, none of the data generated from samples are uploaded to public data banks. The consortium also enforces dynamic consent, meaning that study participants can decide to remove their samples or data at any time through an online portal.
Investigators who want to work with the Native BioData Consortium need to have established a partnership with the Native American communities, says Tsosie. Approved investigators will then receive assistance in navigating the laws of Tribal Nations and policies to engage in ethical research.
Tsosie sees a way forward for microbiome research involving Indigenous communities only if there is a tangible benefit to the people who provide the potentially money-making data, such as investment in community health training or immediate access to any drug or other product that the research has helped to create. “I’m not talking a long-term promise a couple decades down the line,” she says. “Our peoples need health solutions that work for us now.”
![A green metal outbuilding in an expansive grassy landscape. The only other object in view is an orange construction truck parked next to the building.](./assets/OOrICJHNE7/1_native-biodata-consortium-new-genomic-biorepository-and-lab-facility-4032x3024.jpg)
The Native BioData Consortium hopes to open an expanded laboratory and genomic biorepository later this year. Credit: Jace Lindemann
The Native BioData Consortium hopes to open an expanded laboratory and genomic biorepository later this year. Credit: Jace Lindemann
Concerns about unethical collection, storage and use of Indigenous data were a big motivator for the formation of the Native BioData Consortium. Founded in 2018, it is the first non-profit research institute in the United States run by Indigenous scientists and community members.
The group manages a biobank located on sovereign Native American land in Eagle Butte, South Dakota. The consortium stores a variety of biological and non-biological samples and data in partnership with collaborating Native American communities. “Having the biobank on sovereign Native land, where tribal laws and resolutions are in place, can afford additional protection for Indigenous communities who wish to engage in biomedical and other types of research,” says Tsosie, who is a co-founder and board member of the consortium. Fox and Anderson are also board members.
![A green metal outbuilding in an expansive grassy landscape. The only other object in view is an orange construction truck parked next to the building.](./assets/OOrICJHNE7/1_native-biodata-consortium-new-genomic-biorepository-and-lab-facility-4032x3024.jpg)
The Native BioData Consortium hopes to open an expanded laboratory and genomic biorepository later this year. Credit: Jace Lindemann
The Native BioData Consortium hopes to open an expanded laboratory and genomic biorepository later this year. Credit: Jace Lindemann
Unlike at the Microbiota Vault, none of the data generated from samples are uploaded to public data banks. The consortium also enforces dynamic consent, meaning that study participants can decide to remove their samples or data at any time through an online portal.
Investigators who want to work with the Native BioData Consortium need to have established a partnership with the Native American communities, says Tsosie. Approved investigators will then receive assistance in navigating the laws of Tribal Nations and policies to engage in ethical research.
Tsosie sees a way forward for microbiome research involving Indigenous communities only if there is a tangible benefit to the people who provide the potentially money-making data, such as investment in community health training or immediate access to any drug or other product that the research has helped to create. “I’m not talking a long-term promise a couple decades down the line,” she says. “Our peoples need health solutions that work for us now.”
A higher standard
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In the United States, collecting human microbiome samples requires informed consent, as well as approval from an institutional review board (IRB) that provides regulatory oversight. Most researchers meet this bar; those who don’t are criticized by the community.
In 2014, for example, microbiome researcher Jeff Leach made waves when he used a turkey baster to give himself a faecal microbiota transplant (FMT) using faeces from a Hadza man. By 2015, some researchers who had previously collaborated with Leach, including Knight, had distanced themselves from him. As Knight recalls, he heard concerns from other researchers who worked with the Hadza that Leach was not obtaining the proper permits or consent from participants. His self-administered FMT, Knight says, was something that “our research-ethics group would certainly not have allowed”.
By this time, however, many of the samples Leach had collected had already been sequenced and the data made publicly available. Additional samples still sit in lab freezers; Knight has some of them. At one point, Knight hoped that there might be a way of retroactively obtaining approval and consent, but now he expects that the samples will be destroyed. “There is no ethical path forward to using them that I’m aware of,” he says.
Although most researchers obtain IRB clearance for their work, they could still aim higher. “We need to really separate what is legal versus what is ethical,” says Crittenden. IRBs are just a legal minimum, and can be inconsistent, she says. “You can be absolutely above board legally and be conducting unbelievably unethical research in a community.”
For this reason, the Native BioData Consortium requires that the researchers whom it works with adhere to a higher ethical standard. Projects must be approved not just by an IRB, but also by a council of Tribe officials to ensure that the people providing samples will benefit. Tsosie has received some push-back from scientists on this community consent process. “It’s often considered incongruent with the academic pathway of research,” Tsosie says. Researchers, who are under pressure to publish frequently, don’t think they have the time for it. “You get researchers who are like, ‘Oh, that’s too much work. And, you know, I technically don’t need to do it’,” she says.
When Crittenden decided to stop collecting biological samples from the Hadza, she embarked on a course of re-education. “I had to learn how to be a different scientist,” she says. “I had to learn different methods and methodologies. I had to learn different lines of enquiry. And honestly, I had to slow down.” For ethical standards to improve, she thinks that researchers need to be willing to move more slowly, despite incentives to do the opposite.
Funding agencies could be key to enabling researchers to take the time to do things properly. “As a scientific community, globally, we need to be thinking more about the fact that building relationships is part of the work,” says Anderson. Accounting for that time in the funding provided to researchers, he says, would make a big difference to the relationships between investigators and the communities that they study.
Although the field still has a way to go, Crittenden has seen improvements since she first decided to stop collecting biological samples from the Hadza ten years ago. At the time, when giving talks at various institutions, she remembers being asked to avoid talking about community-based research and ethics. “They invited me there for a scientific talk, not an ethics talk,” she says. But over the past few years, she has witnessed a change. Crittenden and other researchers, including Fox, Tsosie and Anderson, have published articles5–7 relating to ethical research with Indigenous communities, and there has been an uptick in the frequency of conversations related to such research, she says.
“When you know better, you do better,” she says, referencing a quote from US author and civil-rights activist Maya Angelou. Helping researchers ‘know better’ is something Crittenden takes seriously. “The responsibility is on me to articulate why this is necessary, why this is a critical step forward and why your science is better for it.”
doi: https://doi.org/10.1038/d41586-024-02792-w
![Alyssa Crittenden sits at a table and smiles at the camera, with mutlicoloured windows behind her.](./assets/tWbleoCw8z/13_d74477_012-alyssa-crittenden-4096x2732.jpg)
Alyssa Crittenden wants to help other researchers to operate more ethically. Credit: Josh Hawkins/UNLV
Alyssa Crittenden wants to help other researchers to operate more ethically. Credit: Josh Hawkins/UNLV
"We need to be thinking more about the fact that building relationships is part of the work.”
In the United States, collecting human microbiome samples requires informed consent, as well as approval from an institutional review board (IRB) that provides regulatory oversight. Most researchers meet this bar; those who don’t are criticized by the community.
In 2014, for example, microbiome researcher Jeff Leach made waves when he used a turkey baster to give himself a faecal microbiota transplant (FMT) using faeces from a Hadza man. By 2015, some researchers who had previously collaborated with Leach, including Knight, had distanced themselves from him. As Knight recalls, he heard concerns from other researchers who worked with the Hadza that Leach was not obtaining the proper permits or consent from participants. His self-administered FMT, Knight says, was something that “our research-ethics group would certainly not have allowed”.
By this time, however, many of the samples Leach had collected had already been sequenced and the data made publicly available. Additional samples still sit in lab freezers; Knight has some of them. At one point, Knight hoped that there might be a way of retroactively obtaining approval and consent, but now he expects that the samples will be destroyed. “There is no ethical path forward to using them that I’m aware of,” he says.
Although most researchers obtain IRB clearance for their work, they could still aim higher. “We need to really separate what is legal versus what is ethical,” says Crittenden. IRBs are just a legal minimum, and can be inconsistent, she says. “You can be absolutely above board legally and be conducting unbelievably unethical research in a community.”
For this reason, the Native BioData Consortium requires that the researchers whom it works with adhere to a higher ethical standard. Projects must be approved not just by an IRB, but also by a council of Tribe officials to ensure that the people providing samples will benefit.
Tsosie has received some push-back from scientists on this community consent process. “It’s often considered incongruent with the academic pathway of research,” Tsosie says. Researchers, who are under pressure to publish frequently, don’t think they have the time for it. “You get researchers who are like, ‘Oh, that’s too much work. And, you know, I technically don’t need to do it’,” she says.
When Crittenden decided to stop collecting biological samples from the Hadza, she embarked on a course of re-education. “I had to learn how to be a different scientist,” she says. “I had to learn different methods and methodologies. I had to learn different lines of enquiry. And honestly, I had to slow down.” For ethical standards to improve, she thinks that researchers need to be willing to move more slowly, despite incentives to do the opposite.
Funding agencies could be key to enabling researchers to take the time to do things properly. “As a scientific community, globally, we need to be thinking more about the fact that building relationships is part of the work,” says Anderson. Accounting for that time in the funding provided to researchers, he says, would make a big difference to the relationships between investigators and the communities that they study.
![Alyssa Crittenden sits at a table and smiles at the camera, with mutlicoloured windows behind her.](./assets/tWbleoCw8z/13_d74477_012-alyssa-crittenden-4096x2732.jpg)
Alyssa Crittenden wants to help other researchers to operate more ethically. Credit: Josh Hawkins/UNLV
Alyssa Crittenden wants to help other researchers to operate more ethically. Credit: Josh Hawkins/UNLV
Although the field still has a way to go, Crittenden has seen improvements since she first decided to stop collecting biological samples from the Hadza ten years ago. At the time, when giving talks at various institutions, she remembers being asked to avoid talking about community-based research and ethics. “They invited me there for a scientific talk, not an ethics talk,” she says. But over the past few years, she has witnessed a change. Crittenden and other researchers, including Fox, Tsosie and Anderson, have published articles5–7 relating to ethical research with Indigenous communities, and there has been an uptick in the frequency of conversations related to such research, she says.
“When you know better, you do better,” she says, referencing a quote from US author and civil-rights activist Maya Angelou. Helping researchers ‘know better’ is something Crittenden takes seriously. “The responsibility is on me to articulate why this is necessary, why this is a critical step forward and why your science is better for it.”
doi: https://doi.org/10.1038/d41586-024-02792-w
References
- Schnorr, S. et al. Nature Commun. 5, 3654 (2014). Article
- Pollom, T. R., Cross, C. L., Herlosky, K. N., Ford, E. & Crittenden, A. N. Am. J. Hum. Biol. 33, e23455 (2021). Article
- Herlosky, K. N. & Crittenden, A. N. Am. J. Hum. Biol. 33, e23593 (2021). Article
- Campbell, R., Hauptmann, A., Campbell, K., Fox, S. & Marco, M. L. Microbiome Res. Rep. 1, 5 (2022). Article
- Claw, K. G. et al. Nature Commun. 9, 2957 (2018). Article
- Mangola, S. M. et al. Nature Microbiol. 7, 749–756 (2022). Article
- Bader, A. C. et al. Nature Microbiol. 8, 1768–1776 (2023). Article
Author: Sam Jones
Illustration: Antoine Doré
Video: Edward Hernandez (camera), Emily Bates (editor)
Art director: Mohamed Ashour
Picture editors: Kezia Levitas, Madeline Hutchinson
Subeditors: Jenny McCarthy, Joanna Beckett
Project manager: Rebecca Jones
Editor: Richard Hodson
This article is part of Nature Outlook: The human microbiome, a supplement produced with financial support from Yakult. Nature maintains full independence in all editorial decisions related to the content. About this content.
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For several decades, Yakult has maintained its commitment to improving human health by researching lactobacilli and through the development of its food, cosmetics and pharmaceutical businesses.
Yakult Central Institute has been conducting a wide range of studies in gut microbiota, probiotics, intestinal immunity and other areas of basic research. Above all, the Institute works to understand the relationship between human health and gut microbiota, focusing on basic research into the structures and functions of microbiota.
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