Perspective

https://doi.org/10.1038/s41564-022-01116-w

Ethical microbiome research with Indigenous

communities
Shani Msafiri Mangola1,2,3, Justin R. Lund4,5, Stephanie L. Schnorr   6,7 and Alyssa N. Crittenden   2,8 ✉

Human–microbiome interactions have been associated with evolutionary, cultural and environmental processes. With clinical
applications of microbiome research now feasible, it is crucial that the science conducted, particularly among Indigenous com-
munities, adheres to principles of inclusion. This necessitates a transdisciplinary dialogue to decide how biological samples
are collected and who benefits from the research and any derived products. As a group of scholars working at the interface
of biological and social science, we offer a candid discussion of the lessons learned from our own research and introduce one
approach to carry out ethical microbiome research with Indigenous communities.

L
arge-scale cross-cultural microbiome research has identi-
fied links between human microbiomes and local ecologies.
Furthermore, the microbiota of Indigenous peoples have been
targeted for basic research, thus necessitating the discussion and
implementation of ethical practices akin to those already set forth in
human genetics research1–6. Many social scientists have been writ-
ing about the demand for more ethical participatory work and pro-
viding research guidelines since the 1960s7–10, with a resurgence in
recent years11–13. Increasingly, Indigenous communities are develop-
ing research-based codes of ethics14–16, including for short-term visi-
tors who will not participate in long-term community engagement.
Beyond the need to address the potential threat of biopiracy in
microbiome sciences, we argue that it is not only possible but cru-
cial to adopt a more inclusive research praxis when working with
Indigenous communities. Here we report our individual motiva-
tions to write this Perspective (Box 1) and propose strategies that
we have successfully used to foster community inclusion.
Improving collaboration with Indigenous communities
The history of how Indigenous communities have been subject to
unethical behaviour by researchers is well documented17,18. As indi-
geneity is often defined through a people’s contact with a colonizing
entity, a power differential remains today owing to past atroci-
ties and ongoing dispossession of peoples from social and natural
resources. Despite increasing calls for more ethical research, there
is scant actionable advice on what community-inclusive research
in biological sciences (other than genetics/genomics) looks like or
how to establish long-term partnerships and benefit-sharing agree-
ments. The core principles of collaboration, representation and
capacity building are publicized as key, but without a framework
of accountability, these principles remain challenging to actualize.
Although there is no one universal set of standards, there are
actions that researchers can take that will improve protocols. Here
we share suggestions that we hope will encourage more inclu-
sive and ethical research practices in the microbiome sciences. In
addition, we present some commonly asked questions about the
practicality of applying ethical standards in human microbiome
research (Box 2).
Community-based participatory research (CBPR) is defined in
myriad ways15,18 but is most generally understood as research that
includes the community at the outset of the project, ideally with the
community approaching research teams and requesting particular
work to be done that supports community needs. Although CBPR
is generally less common in human biological sciences, its practice
(particularly in the social, health disparities and sustainability sci-
ences) is becoming the gold standard for any research conducted
with Indigenous communities19–23.
Community-inclusive approaches (not the same as CBPR)
should be informed by an existing relationship with the partici-
pant community. If no relationship exists, researchers should ask
themselves ‘why do we want to undertake work with this specific
community?’ and ‘what are our goals, rationale and theoretical justi-
fications that make this particular community ideal for the intended
research?’. This may seem a challenging principle to adhere to as
many researchers do not have relationships with the participating
communities, so one solution may be to engage in pilot research or
collaborate with researchers who already have existing relationships
with the participating communities.
We outline actions that will facilitate ethical microbiome sam-
pling and propose that these actions may also be applicable to bio-
logical sampling in general.
Culturally appropriate sample collection protocols are
needed
Biospecimen sampling can often be repetitive, invasive, a source of
discomfort and may lead to community research fatigue, meaning
that participants can experience research requests as an intrusion.
One way to mitigate this is to ensure that the sample collection pro-
tocols have been pre-approved by the participant community. It is
possible to include funding requests for the collection of pilot data,
field-testing instruments, building community relationships and
incorporating community input. These early activities and their

1
Indigenous Peoples Law and Policy Program, James E. Rogers College of Law, University of Arizona, Tucson, AZ, USA. 2Olanakwe Community Fund (USA),
Boulder City, NV, USA. 3Olanakwe Community Fund (TZ), Mang’ola Ward, Karatu, Tanzania. 4Center for the Ethics of Indigenous Genomics Research,
University of Oklahoma, Norman, OK, USA. 5Laboratories of Molecular Anthropology and Microbiome Research, Department of Anthropology, University
of Oklahoma, Norman, OK, USA. 6Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria. 7Center for Microbiology and
Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria.
8
Laboratory of Nutrition and Reproduction, Department of Anthropology, University of Nevada, Las Vegas, NV, USA. ✉e-mail: alyssa.crittenden@unlv.edu

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Perspective
Box 1 | Authors and motivations
To acknowledge the intersectional identities of all contributors to
this work and as an explicit attempt at reflexivity, we document
our individual perspectives for how and why we have come to un-
derstand a need for promoting equitable partnerships in microbi-
ome research.
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, advocating for the
equitable education of Hadzabe children who want to attend
school in Tanzania. My motivation to co-author this paper 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.
Researchers often begin working with a community and are
only there to collect short-term data, assuming that this means
that they do not have a responsibility to learn about the cultural
history of the community and the power structures at play in the
host country. My people, for example, are facing land disposses-
sion, the destruction of our livelihood, extreme poverty and lack
of access to education, healthcare and political decision-making.
Scholars and others who write about Hadzabe people as ‘locked
in time’ do nothing to support our right to self-determination.
Terms such as ‘primitive’, ‘non-modern’, ‘ancestral’ and even ‘tra-
ditional’ can be used as a means to dispossess us from our land
and resources (both natural and state-provided). Highly publi-
cized research, such as the work of microbiome scientists, has the
ability to either benefit the study populations or further margin-
alize them in their own nations and beyond. I participate in the
writing of this paper so that my position is published. Although
I am Hadzabe, I do not speak on behalf of my community. I am
contributing here because my community is still struggling for
basic legal recognition, and any scholarship that depicts some
groups of people as closer to nature means that they are, whether
intentionally or not, being depicted as less worthy of the rights
readily granted to those in the post-industrialized west.
Justin R. Lund. I am Diné of the Navajo Nation from Ganado,
Arizona. In addition, I am a PhD candidate in the Department
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of Anthropology at the University of Oklahoma, where I am also
a research scientist for the Center for the Ethics of Indigenous
Genomics Research, an NIH-funded Center of Excellence in
ELSI Research. My research and work explore the intersection
of genomics, Indigeneity and bioethics with the specific aim
of elevating the Indigenous perspective and voice to ultimately
empower Indigenous forms of sovereignty.
My hope as a co-author in this manuscript is to bring to the
surface an important topic that can often get pushed aside, par-
ticularly in research. For me, the most basic question we should
be asking when working with Indigenous or other marginalized
communities is ‘who benefits from this [research]?’. In the future,
the answer to that question will be most obvious, and hopefully
this Perspective contributes to that realization. Without a doubt,
the people who should benefit most from research are those being
researched.
Credit: Trip Steilher
Unequal benefits from research practices only contribute to
the long-standing tradition of marginalizing Indigenous people.
I believe that confronting these painful truths can be fruitful and
mitigate the potential of future harmful research and marginal-
ization. In a very real way, the relationship between Indigenous
peoples and outsiders becomes entrenched in the historic relation-
ship between Indigenous ancestors and their colonizers. This rela-
tionship does not begin anew with each new encounter or research
idea; only new actors are incorporated. Careful nurturing of this
troubled relationship can foster a future that benefits everyone.
Stephanie L. Schnorr. I am a biological anthropologist, a
non-Indigenous white female trained in US and European insti-
tutions, and I became involved in human microbiome research
through the study of human diet. Working with a hunter-gatherer
community is very attractive from the standpoint of trying to
understand the human physiological capacity to survive on foods
gathered in the wild. Early on, I was easily assuaged against the
idea of exploitation by the process of informed consent and was
not cognizant of building the transactional relationship that allows
the participant community to participate in dictating the aims of
the research. In this regard, I was uninformed about what it means
to be working alongside Indigenous community members to
further research goals. I did not fully appreciate that I would be
working with other people who would have opinions about the
relevance of my work to them. My understanding of benefits and
power disparity from research relationships changed when I saw
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Box 1 | Authors and motivations (continued)
how much media and public interest grew around the subject of
Hadza microbiome research. The majority of this dialogue cen-
tred on how the microbiome data from Indigenous peoples could
be used to improve the health of westernized people, with little
interest given to understanding the role of the microbiome in the
context of the health of the people under study.
Credit: Erwin Becker
My motivation to co-author this paper is to help other research-
ers like myself achieve this awareness earlier than I did and to real-
ize the responsibility of working in partnership with participant
communities. In this way, consent is a continual process built
from mutual interest and engagement in the work at hand. I also
contribute to this paper to help counter misconceptions about the
perceived benefits of extractive human microbiome research and
challenge the mythical narratives—propped up as scientific con-
cepts—of ‘wild’, ‘unperturbed’ or ‘ancestral’ states of the human
microbiome that represent idealized scenarios for health
optimums.
Alyssa N. Crittenden. I come to this work as a non-Indigenous
woman. I am descended from European and Mexican immi-
grants. As a white-presenting professional in academia, I want to
acknowledge that I have undoubtedly benefited from white privi-
lege. I have expertise and training in nutrition, ecology, human
biology and anthropology (a discipline that was founded on settler
colonialism16). I want to publicly acknowledge, in a space that is
rationale are crucial methodological steps, and their publication
in full alongside the primary work supports the scientific process
(an example is provided in ref. 24). This services participants by
minimizing the discomforts associated with sampling (for example,
invasion of privacy, sensitivity or pain from body contact, and so
on) and full methodological transparency improves reproducibility.
It signals to future potential researchers the considerations and time
that are necessary when conducting human microbiome research
with Indigenous communities.
Use of tiered informed consent
Obtaining informed consent is a crucial component of all research
involving people. The level of understanding, from the purpose of
the proposed project to the risks and benefits of participation, can
vary widely. The familiarity of the participant community with the
research practices and the power dynamics between researchers and
the researched are important factors that can affect voluntariness
of participation25,26, which university institutional review boards
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Perspective
read and cited by those engaging in research on the microbiomes
of Indigenous peoples, that my own past research practices were
rooted in colonial nostalgia55.
Credit: Cate Weeks
My initial motivation to participate in the writing of this
Perspective was in acknowledgement of mistakes in my own
research past, particularly regarding the language used to describe
the way of life of the people of the Hadza community in Tanzania,
whom I have worked with for eighteen years. In some previous
works I co-authored harmful language was used to characterize
the hunting and gathering economy of the Hadza as akin to an
‘ancient traditional lifestyle’35. I want to be part of the push for
changes in not only terminology but practices employed in bio-
logical research. I have realized, with some very pointed and clear
input from interlocutors and members of the Hadza commu-
nity, that I was complicit in the construction of the narrative that
Hadza gut microbiota (and thus the hosts themselves) were some-
how closer to our evolved state than those of us in North Atlantic
populations. I have described elsewhere56 the details of my willing
departure from microbiome science for the time being and my
shift to community-based and community-inclusive work.
I have made mistakes and, while I will most likely make them
again, I am actively working on bettering my research methods
and academic research in the hopes of a stronger and more ethical
commitment to biological research done in collaboration with and
at the request of Indigenous communities.
(the body typically approving consenting procedures) may not be
able to properly assess. A robust literature on the ethics of consent
processes and biobanking already exists (full summary in ref. 27).
It is our aim here to briefly summarize how iterative learning, or
tiered consent, can work to not only facilitate improved under-
standing of the research project but also foster greater trust between
participants and investigators.
In recent years it has become increasingly common for bio-
logical scientists to use ‘broad consent’, which means obtaining
participant authorization for a study-specific research project
as well as use and disclosure permissions for future unspecified
research purposes. Alternative types of consenting procedures are
increasingly being called for—particularly when working with
Indigenous communities and/or when engaging in commercial or
for-profit research28,29. One such procedure, called iterative learn-
ing consent, entails multiple passes and sustained communica-
tion between the investigators and participants. At multiple stages
of the project, investigators obtain consent from participants
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Perspective
Box 2 | Q&A on ethics in microbiome research
Note that this text is modified from real Q&A dialogues experi-
enced by the authors.
Q1 How are words like ‘traditional’, ‘ancestral’, ‘wild/re-wild’,
‘non-modern’, ‘uncontacted’ or ‘non-industrial’ problematic? I am
not using derogatory language like ‘primitive’, ‘ancient’, ‘bushmen’ or
‘backwards’, and I know that all living humans are modern people.
A1 These terms invoke a mythical narrative, much like Rousseau’s
idea of the ‘noble savage’ (see ref. 57 for a history of the term),
that there is an idealization to be found in the deep human past.
The narrative centres on the idea that given populations exist
in ‘harmony with nature’, an idea based on an invocation of the
evolutionary ecology of pre-Anthropocene human ancestors.
Such populations are often used as models for proxies of how we
evolved—and thus how our inner ecologies ‘should be’ today.
The re-wilding concept is predicated on the imagery of ‘wild’
and ‘closer to nature’, to which the basis of ‘re-wild’ is applied.
The word ‘traditional’ is imprecise and begs the questions ‘what
traditions?’ and ‘whose traditions?’. Words like ‘ancestral’ and
‘intermediate’ set up a false assumption about the historical and
genetic links between individuals over time. This is based on
concepts of linear evolution: the idea that there is a linear gradient
of human subsistence activity. This harkens back to racially
motivated social-Darwinian thinking of the 19th century. Every
population that is studied in the 21st century is contemporary
and influenced by the global economy as well as the nation state;
to suggest otherwise is not only scientifically inaccurate (and
overlooks important ecological variables that should be measured)
but may be offensive or harmful to the participating populations.
Indigenous donor communities are tacitly implied to be the
model ‘ancestral’ state, and they are often promoted as harbouring
ecological resources that require action in conservation attempts
so that they can be harvested by wealthy and powerful entities to
replenish their own lost natural resources.
The word ‘uncontacted’ is also highly problematic as it is often
applied to rural communities (often with a low degree of market
integration), implying that they have never encountered ‘outsiders’
despite the fact that the researchers themselves are somehow
there (with all of the necessary permits, visas and guides that
can lead them to these ‘uncontacted’ villages or encampments).
Critically, the theme of ‘uncontacted’ thus disregards centuries
of population-level interactions that all human groups have
maintained throughout human history.
Q2 Microbiome science has a strong conceptual basis grounded
in the evolutionary and ecological sciences; therefore, researchers
are rightly endeavouring to characterize the implications of altered
microbiome assemblies that are observed among [westernized]
societies for human health and work towards solutions. For this,
we need referential community data and samples, and we should
use an evolutionary framework.
A2 Disruption and altered community assembly in an evolutio­
nary or ecological context is not contingent on small-scale
sampling of microbiomes of Indigenous communities, nor are
disruptions observed among westernized societies necessarily
understood through an evolutionary lens. Disruption happens
in all communities when diet and lifestyle changes occur. To
suggest that this is a west versus hunter-gatherer dichotomy
is scientifically inaccurate and remains harmful to participant
communities as it works on the supposition that the microbiomes
of hunting-and-gathering populations are ancestral. Moreover,
the field is still grappling with rationales for sound theoretical
approaches when it comes to characterizing the differences and
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implications of human microbial ecologies in conjunction with
human-behavioural ecologies58.
Q3 If these ethical guidelines are implemented, they would just
result in more bureaucratic burden. This work may potentially help
the very communities under study. CBPR and contracting benefits
sharing is arduous and will take years to establish. How can the
scientific community be expected to operate within these guidelines?
A3 The burden should be on the scientists to ensure that the
participant community is incorporated into research design,
has a clear understanding of the research in question, agrees to
the use of data and who will have ownership of such data, and
is compensated accordingly for their labour. Calling the basics
of ethical engagement ‘bureaucratic burden’ is problematic given
that it is neither consistent with the foundational regulatory
policy for research ethics59 nor cognizant of implicit biases in
agenda prioritization. Rather, following higher standards of ethics
is possible and will produce better scholarship.
All scientists who conduct research by a certain set of values
and standards should acknowledge that these are culturally and
institutionally constructed and that the instantiation of values by
participants is a reality that needs to be considered. The agenda
of research is not a priori to be valued and conducted. Work with
Indigenous communities must be driven by a strong theoretical
justification and a commitment to carefully negotiate transparent
contracts with group representatives. This is accomplished through
collaboration with the community. When such relationships do
not already exist, researchers should collaborate with represen­
tatives and/or long-term community-based researchers to begin
communication with the participant communities.
Q4 I compensated all of the participants according to a rubric
that was neither coercive nor exploitative, and everyone seems
happy with the exchange. Why do I need a benefits-sharing contract
to work with Indigenous people and to commit to provide even
more benefits to them than what would normally be provided in a
study involving, for instance, undergraduate students at my local
university? My ethics training through my institutional review
board demonstrated that the promise of benefits can be coercive
and therefore unethical, so how does a benefits-sharing agreement
enable high-quality, unbiased, ethical research?
A4 Compensation is handled within the participatory frame­
work of negotiating the relationship between researchers and
communities and establishing the basis for the work. Indigenous
communities are often disadvantaged in the research arrangement;
they do not necessarily benefit from the conducted research
and may not be fairly compensated for the advances that their
contributions have made.
The disclosure of compensation is essential in the consenting
process and may necessarily occur at different levels (community,
group, family, individual, and so on) but must be comprehensive
and transparent so as to be equitable for all potentiation of
research and returned benefits. Transactional relationships should
be carefully embedded within research study development and
procedures5. An example of a high-profile case of microbiome
biopiracy that demonstrates how exploitation can creep into what
may appear as scientific enterprise, and why it is critical to address
and rectify perpetuating disparities, is discussed in ref. 60.
We also emphasize that benefit sharing is distinct from
compen­sation, although there may be some overlap in practice,
which is clearly outlined in the Nagoya Protocol. The Nagoya
Protocol, adopted in 2010 by the United Nations Convention on
Biological Diversity, represents a move towards equity in research
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Box 2 | Q&A on ethics in microbiome research (continued)
practices. The Protocol establishes an international framework for
benefit sharing of the natural resource of genetic material53. The
Convention on Biological Diversity clearly articulates that benefits
from biological resources are fairly shared according to mutually
agreed terms between participant communities, researchers and
commercial entities.
Although the Nagoya Protocol sets a standard for fair use
and access to resources, it abstains from highlighting gaps in the
practicality of implementing its procedures. Therefore, the vision
of capacity building set forward by the Nagoya Protocol would
happen at state levels and would rarely (at this time) benefit
Indigenous groups. The responsibility of researchers is instead to
focus on benefits sharing and capacity building that are realized
by the donor community, not necessarily the state, as the relations
between donor communities and nation states may be contentious
(comment by S.M.M. in Box 1).
Q5 Open science and data policies are positive trends in scien­
tific research that help to promote equitability in science across
career stage and social or political strata. The human microbiome
is the property of everyone. Some human tissues are literally
excrement, and I am studying the microbiota, which come from
the environment anyhow. Therefore, what is wrong with storing the
in a stepwise fashion, facilitating improved understanding of
the research being undertaken at the time of recruitment and
throughout the life of the project. Although the specifics of the
process will differ depending on the project, the framework entails
regular communication, corrective feedback from the participant
communities and repetition of information to facilitate greater
understanding of the research aims.
In some instances, as is the case with biological samples, explicit
discussion of permission for storage and future use is necessary.
This is particularly true in regard to microbiome research due to
the dispersed nature of the raw sample (an ecology of non-host
molecules) as well as the longevity and transmissibility of the digi-
tal data29. One way to engage in this type of iterative process is to
convene a community advisory group that can act as a sounding
board to researchers and provide guidance for future research and
continued communication30. This type of approach also moves away
from an exclusively individual-based consent approach, which often
acts to sidestep aims to engage in CBPR and can work to undermine
Indigenous sovereignty31.
Share results with the participant community
The practice of returning research results to the participating
communities is not new32. In regard to genomic research, many
countries and international bodies have laws and regulations that
require the return of research results to the participants. Although
this debate is complex and contentious, a rights-based approach
to research necessarily includes the return of results to the partici-
pating communities2,4. The feasibility of such a practice includes
advance planning, as many granting institutions (for example, the
National Science Foundation, the National Institutes of Health)
will often fund return trips to report results if travel expenses
are included in the initial budgets. Although this practice has
increased in other biological disciplines, it is not yet widely prac-
ticed with microbiome studies. Research participants have a right
to the knowledge generated about themselves (see the discussion
of data sovereignty in the ‘Publicly acknowledge the contributions
of the participants’ section), and results sharing allows all par-
ties to have access to the knowledge that was generated by the
working relationship.
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Perspective
samples that I collected and thinking about how the information
they provide can be applied to help all humans? More data and
more sharing are always better.
A5 Data sharing requires that sound infrastructure, usage
policies and oversights are in place to ensure that the process of
open data is actually a fair one. Furthermore, although open data
access is one step towards levelling inequities for scientific process,
the resource divide between high- and low-income nations still
means that the source communities and countries of these data
may also be technologically disenfranchised and unlikely to be
able to use or commission the use of their own contributions.
The problem with the concept and rhetoric of ‘universal
ownership’ is that it objectifies group-characterizing biological
or cultural features and alienates these features from their origin
community members. Extracted data may be seen as “more
suitable for preservation in museums patronized by exceptionally
discerning elites than for ordinary use in everyday life by imperfect
human beings”61. Universal ownership concepts also imply
belief in a ‘common humanity’ with a shared agenda and that the
natural and cultural elements of the world need to be preserved
through ownership or stewardship, further promoting colonial
enterprise.
Publicly acknowledge the contributions of the participants
Community contribution in the research study should be widely
and publicly acknowledged. This includes in publications on pub-
licly available data-sharing sites (if permission was granted for data
sharing) and in media coverage of the research.
Acknowledgement of research assistance is central to capacity
building and ethical scientific engagement. If local research assis-
tants help to obtain data reported in a peer-reviewed publication,
they should be offered authorship12 (although authorship may not
necessarily be a useful form of compensation, depending on the
population, project, and so on; see the discussion in the ‘Establish
benefit-sharing relationships’ section). Acknowledging the work
relationship between a community and scientists fosters trust, can
benefit the careers of the research assistants and community data
collectors, and ultimately holds the scientists accountable to the
participating community.
Use accurate, respectful language to describe participant
communities
Language and representation matter. Participating communities need
not be exoticized and labelled as closer to nature to make the point
that microorganisms and humans have co-evolved mutually ben-
eficial relationships. It is worth noting that the health of Indigenous
communities, including the microbial ecosystems that they host, have
often already been disrupted as a consequence of colonial legacies
and increased market integration33,34. We suggest the following two
ways to ensure that appropriate characterization is achieved.
Replace the word ‘traditional’. Many of the communities that have
contributed samples to the booming industry of cross-cultural
microbiome science are often described using language that not
only romanticizes their connection to their ecological environment
but also indicates that they are somehow proxies for the ancestral
microbiome. Indigenous participant communities are often labelled
as ‘non-modern’, ‘non-industrial’ or ‘traditional’. Some of us (A.N.C.
and S.L.S.) have used such language in the past35 and are now publicly
acknowledging our errors in doing so (discussion in Box 2). What
do we, as scientists, really mean when we say ‘traditional’? There is
no articulation of what ‘traditional’ typically means, leaving it to be
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loosely interpreted as being ‘anything outside of post-industrialized
westernization’ (Box 2).
Specific attention should be paid to how communities are
described. Ultimately, microbiome research aims to understand the
ecologies of microorganisms in human populations.
Cultivating microbiomes means cultivating a microbial environ-
ment or, in other words, the ‘environment of traditions’. As such, we
should turn the dichotomy of ‘traditional’ versus ‘non-traditional’
into simply a question of ‘what traditions help to construct the
environmental context in which the observed microbiome features
establish and persist?’36. This means that blanket descriptions of
communities as ‘traditional’ are replaced with specific discussion of
what cultural practices or ecological contexts make the participat-
ing community particularly worthy of study (discussion in Box 2).
Use the name of the participant community. The specific name
of the community, if a single population is under study, should be
included in the title of the paper. For example, if writing a paper
about Hadza foragers, the name of the population should be in the
title rather than ‘African foragers’, as there are dozens of candidate
populations for which that moniker could apply. Naming the partic-
ipating population upfront not only acknowledges the contributions
of that specific community but demonstrates that the research being
published is not necessarily a blanket statement about all foragers or
all African foragers, and so on.
It is also important to provide adequate details on the recruit-
ment methods used so that it is clear which subset of a community
or population provided samples, as sampling an entire population is
often not feasible. Identifying information should not be shared, but
adequate information clearly articulating who the participant com-
munity is should be required in all scientific publications.
We can use discussion of hunter-gatherers to illustrate the sig-
nificance of using appropriate language. Foraging communities
often exist on a continuum of market integration and consume
mixed-subsistence diets (not an exclusively wild-food diet but also
one that incorporates processed and domesticated foods; see refs. 37–39
for rare acknowledgement of this continuum). The Yanomamö,
for example, are often listed as hunter-gatherers who are “not
impacted by urban-industrialized lifestyles”40. They are, in actual-
ity, a large ethnic group spanning multiple countries with varied
degrees of market economy, all of whom practice mixed subsis-
tence horticulture, tend gardens and, in some cases, have access to
medical care and work in cities. All of this information has been
published widely since the 1970s across the social sciences and in
popular media—with sustained interactions between the com-
munity and anthropologists, missionaries, government officials
and representatives from extractive industries41–44. However, the
Yanomamö are often portrayed (regularly in high-impact scientific
journals) as uncontacted, with claims that they have been “relatively
isolated for more than 11,000 years”45. Discussing the Yanomamö
as uncontacted is not only disrespectful to the participants but also
scientifically inaccurate.
Another relevant example is the foraging community of Hadzabe
in Northern Tanzania (tribal affiliation of co-author S.M.M.).
Individuals who identify as Hadza or Hadzabe, for example, speak
Hadzane as their first language, reside in residential encampments in
grass huts in the Lake Eyasi basin, have the same material culture (for
example, bows and arrows, and beaded garments) and collect wild
foraged food for a proportion of their diet. Although these charac-
teristics apply to most Hadza people, the degree to which individuals
or residential encampments have access to purchased/traded foods,
participate in the market economy, engage in wage labour and receive
income from tourists is highly variable46–48. Diet composition is there-
fore critical in any study exploring ecology and/or human health as it
relates to nutrition (this necessarily includes studies on the gut micro-
biome). Without adequate information on which members of a given
754 Nature Microbiology | VOL 7 | June 2022 | 749–756 | www.nature.com/naturemicrobiology
NATure MIcroBIology
community are being sampled, scientifically inaccurate assumptions
can be easily made and participants incorrectly described. Members
of participant communities do indeed read research published on
their communities (as S.M.M. often points out in public fora) and
often identify such inconsistencies—long after publication and with-
out any formal mechanism to report inaccuracies.
Establish benefit-sharing relationships
Abundant examples illustrate historical inequity in community
research relationships, particularly with Indigenous participants
and those from low- or middle-income countries15. Although many
groups compensate study participants for donating biological samples
or participating in research, the benefits that the research team accrue
far outweigh any benefits to donor communities. Contributions of
small monetary compensations or trade items that may be useful (for
example, a cooking pot, blanket, and so on) are paltry compared with
the potential benefits to the careers and livelihoods of the investiga-
tors. The dialogue needs to expand to benefits sharing (see Box 2).
Only scant examples of participant-shared research benefits exist
(see ref. 49 for a discussion of the San-Hoodia case). In microbiome
research, there are even fewer examples of community-engaged
research; however, some notable exceptions exist in which par-
ticipants received health screenings50 or are part of ongoing part-
nerships and collaborative work aimed at benefiting participant
communities51. We stand at a time in scientific exploration where
we must begin to formalize models of what benefits sharing looks
like in a variety of contexts, including in microbiome sciences52.
The concept of profit or benefit sharing has been explored else-
where in great detail, particularly as it pertains to extractive indus-
tries53,54. We have no direct guidelines to point to here, other than
a strong need for such guidelines to be developed—particularly as
the pace of research in microbiome sciences only increases. We
also emphasize that benefit sharing is distinct from compensation,
although there may be some overlap in practice, which is clearly
outlined in the Nagoya Protocol (Box 2).
A research partnership that includes community members
as researchers is of value to the research at hand and to the com-
munity. A well-established reciprocal relationship constructed
with community benefit and capacity building at the centre will
help create a pathway to future research partnerships. In addition,
community-based and -inclusive research infrastructure is nec-
essarily centred on capacity building that promotes Indigenous
scholars. Training and including Indigenous data collectors in your
research design will expand and strengthen the activity and recog-
nition of Indigenous scholars across the sciences.
Conclusions
Confronting the difficulty of incorporating a more ethical research
praxis in cross-cultural microbiome research is immediately nec-
essary such that we bridge the gap between well-intentioned and
well-conducted. Advancing cross-cultural biological research to
inform our understanding of the spectrum of human biology, adap-
tation and experience is an important effort worth pursuing.
We lack explicit answers to the pressing questions of how
transparency and accountability are best achieved and what the
best and most-inclusive consenting procedures are in a variety of
contexts. Answers to these questions are often community- and
project-specific, and must be answered within the course of trans-
parent dialogue between scientists and participant communities.
Our goal in this Perspective is to bring awareness to the field of
microbiome research. We aim to direct attention to the impor-
tant and actionable work already being done in this arena, much
of it by Indigenous scholars2,4,5,34. Our collective perspective here
is borne out of an acknowledgement that disciplines are siloed;
therefore, only through transdisciplinary dialogue and working
alongside Indigenous scientists and participants can we truly work
NATure MIcroBIology
towards a stronger academy. Rather than being held separate and
treated as removed from the process of scientific inquiry, we argue
that the practices we begin to outline here are not only necessary
components of ethical research but are a central component of
scientific rigour.
Received: 25 November 2020; Accepted: 31 March 2022;
Published online: 16 May 2022
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Acknowledgements
This work was funded by a National Science Foundation SBE Postdoctoral Research
Fellowship (award no. 1810060), the European Union’s Horizon 2020 research and
innovation programme under the Marie Skłodowska–Curie grant agreement no.
847693, the National Human Genome Research Institute and the Center for the Ethics
of Indigenous Genomics Research (grant no. RM1HG009042), and the Wenner Gren
Foundation for Anthropological Research. The authors thank those who evaluated
previous versions of the manuscript and provided critical comments, provided
opportunities to present early drafts and fostered insightful discussions throughout the
process of constructing this work: H. Bachner, H. C. Barrett, D. Benyshek, D. Berry, G.
Caniglia, A. Gomez, B. Hewlett, R. Hitchcock, C. Hofman, D. Shopo, J. Indaya, A. Laciny,
W. Lukasi, I. Mabulla, R. Matiyas, S. Strum and D. Western.
756 Nature Microbiology | VOL 7 | June 2022 | 749–756 | www.nature.com/naturemicrobiology
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Competing interests
S.M.M. and A.N.C. declare non-financial competing interests as unpaid board members
for a 501c(3) educational non-profit organization that works with the Hadzabe
community, the Olanakwe Community Fund (www.olanakwe.org). The work of the
mutual aid organization is unrelated to biological research. S.L.S. and J.R.L. declare no
competing interests.
Additional information
Correspondence should be addressed to Alyssa N. Crittenden.
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