Reviving colonial science in ancestral microbiome research

This is excerpted from my paper at the 2016 Crossroads in Cultural Studies conference in Sydney titled “Collapsing the pre-modern and the non-western in ancestral microbiome research,” and comes out of a chapter in my dissertation that examines the colonial logics of scientific research on the ancestral state of humans and their microbial symbionts.

In their research publications, press releases, and pop-culture writings, scientists stress the great importance of the human microbiome (the trillions of microorganisms that live in and on the human body – with concentrated communities in the gut or digestive tract – and provide important physiological functions for their human hosts), and even herald it as the underlying cause of countless aliments. A specific research narrative has developed along this concern, which is the major focus of my dissertation—some scientists studying the microbiome argue that westernization and life in modernity have wreaked havoc on the microbial symbionts of industrialized people.

blaserIn Missing Microbes: How the Overuse of Antibiotics is Fueling our Modern Plagues, Martin Blaser—Professor of Translational Medicine, and Director of the New York University Human Microbiome Program­—writes that amid the medical advances of the twentieth century, including, “improved sanitation, rat control, clean drinking water, pasteurized milk, childhood vaccinations, modern medicinal procedures including anesthesia, and … seventy years of antibiotics,” something has gone terribly wrong. He argues that overuse of antibiotics, consumption of the so-called ‘western diet,’ and lack of exposure to environmental microbes is the cause of a rising number of what he terms “modern plagues.”

These modern plagues include obesity, diabetes, autism, digestive maladies, and a crisis of autoimmune diseases among urban, “westernized” populations. Blaser argues that western populations suffer these conditions in greater numbers because we have lost “old friends,” or, the microorganisms that we co-evolved with and which give our immune system the proper training to defend against legitimate foes.

Blaser, per the title of his book, directs his readers to consider the missing microbes in western bodies, as the key to restoring health. For Blaser, the goal of studying the microbiome under modern life is to “reverse the damage” of such modern plagues, and establish strategies for restoring the missing microbes. One such strategy is to attempt to “define our historic ‘norms’” in terms of microbial communities, so that we might “fill the modern void” and “give them [our ancient microbes] back.”

Following the arguments that impoverished microbiomes of industrialized westerners are the cause of a range of autoimmune disorders, some scientists posit that the answer to this problem is to discover the ancestral state of humans and microbes – before modernity – in order to ‘restore’ Western guts to a state of nature, and presumably, to health.

But how would a scientist study the microbial populations of ancient people? Current tests of the human gut microbiome are done by taking a fecal sample and running the material through metagenomic sequencing, extracting the genetic material of everything in the sample and then attempting to reconstruct “who” is inside the gut based on “who” came out. Microbes are identified from pieces of their DNA that correspond to known species in a database. Because it is not possible to take ‘fresh’ fecal samples from ancient people, ancestral microbiome studies undertake research on living people in rural and under-developed communities in the global south as an appropriate proxy.

This ancestral microbiome research on living people temporally collapses the “non-western” and “pre-modern” research subject. These studies assume that peoples living so-called “hunter-gatherer” lifestyles in places like eastern Tanzania and the Venezuelan Amazon are appropriate biological proxies for humans living 10,000 years ago. This temporal collapse reduces indigenous and rural people living traditional lifestyles to mere research fodder — or “living fossils,” it depoliticizes their existence in the present by writing of them as untouched and uncontacted, and sets up dangerous pathways for bio-prospecting novel microorganisms from the bodies of rural and indigenous peoples of the Global South in order to “restore” the dysbiotic microbiomes of westerners suffering from autoimmune disorders.

The problems in ancestral microbiome research were presaged by problems in human genetic research that scholars Kim Tallbear and Jenny Reardon have outlined in their respective books, Native American DNA and Race to the Finish. The language of “untouched,” “isolated,” and “unique” populations, as well as well as what Tallbear calls the “vanishing indigene” trope are also front and center in ancestral microbiome research on indigenous people.

“The Microbiome of Uncontacted Amerindians” is a 2015 paper from the lab of Gloria Dominguez-Bello that categorizes the gut microbiota of Yanomami people living in Amazonia, in a part of the Amazon rainforest bordered within Venezuela. Although the authors acknowledge that the Yanomami have interacted with rural Venezuelans since the 1960s, they assert that the titular “uncontacted” Yanomami sampled in their article are from a community with “no documented previous contact with Western people.” The authors explain that these Yanomami “inhabit … unmapped [and] uncharted villages” in “vast mountainous” territory. Multiple times they refer to the Yanomami as “isolated” and suggest that these research subjects “have remained isolated for more than 11,000 years.”

Writing about the Yanomami this way would lead the reader to believe that Dominguez-Bello’s research team was the first meeting between this Amerindian group and non-indigenous people. This is, however, untrue. The Yanomami have been studied extensively by western anthropologists, and even sparked a fierce debate within the discipline regarding how research on indigenous populations should be considered from an ethical perspective.

In ancestral microbiome research, isolation equals pureness, which is the same thinking around admixture that troubled human genome scientists. Ancestral microbiome studies use “diversity” of microbial communities as a kind of scale to measure isolation/pureness in the sample population. The Yanomami are frequently described as harboring the most diverse human microbiome – Nature News reports that the Yanomami microbiome was “even more diverse than those reported for other indigenous groups in South America and in Africa.”

The Hadza people living in the Rift Valley of Eastern Tanzania— also studied extensively by European and American anthropologists and biologists—are described in a paper by Schnorr et al as a “rare example of human subsistence through hunting and gathering.” The Schnorr et al paper describes the Hadza as closer to nature in a social and evolutionary timescale; they “maintain a direct interface with the natural environment, deriving their food, water and shelter from a rich biosphere blanketed in the complexity of microbial communities and interactions,” and as a result, the Hadza harbor “extremely rare” microbial phyla and diversity. This gut microbiota diversity, Schnorr argues, “is almost certainly the ancestral state for humans.”

The Schnorr article clarifies that it is the Hadza’s status as a “hunter-gatherer” group that makes them particularly valuable research subjects – they point out a gap in scientific knowledge about microbe and human relations among hunter-gatherer populations, which they write, “is especially problematic because humans have relied on hunting and gathering for 95% of our evolutionary history.” They also seek to “understand how human microbiota aligns with a foraging lifestyle, one in which all human ancestors participated before the Neolithic transition.” The authors suggest that because some Hadza practice food foraging and hunting, they are akin to humans from 95% of evolutionary history before the Neolithic transition. They assume that certain lifestyle behaviors (hunting and gathering food resources) are meaningful enough with regard to human and microbe interaction to represent a pre-modern lifestyle in their research design.

By describing the Hadza as “one of the last remaining hunting and gathering communities in the world” and as a “rare example of human subsistence through hunting and gathering that persists in the same East Africa Region where early hominins lived,” Schnorr et al connect hunting-gathering behaviors of non-western groups to early species of the genus Homo nearly two million years ago.

Claiming to conduct research on “untouched” human communities living in “isolated” enclaves is a powerful way to bring heightened urgency and importance to these microbiome sampling projects. The framework also allows for representing these indigenous groups as part of a world that is disappearing—threatened by modern life. Another researcher notes that the Hadza, and other hunter-gatherer groups like them are “disappearing fast” and that if we don’t act soon to sample and catalogue, “this potential microbial Noah’s Ark will soon be lost.”

The worry here is not that the actual people will disappear but that they will ‘disappear’ as appropriately untouched research subjects on account of their increased participation and interaction with the world beyond their communities. This would alter the ancestral state of their microbiome, and thus the “treasure” or “Noah’s ark” of indigenous gut microbiota would be lost. This is precisely the worry that animated genetic diversity projects; the problem of admixture threatens to eliminate the genetically pure research subjects required to map human migration via DNA. As Reardon and Tallbear explain, this research formalizes the narrative that native peoples and culture were “doomed to vanish before the steam engine of westward expansion,” that their bloodlines were “doomed to vanish through genetic admixture,” and now, their microbial communities are “doomed to vanish” by encroaching modernity.

Attention to vanishing populations of untouched research subjects produces a temporal collapse between the non-western, indigenous body/gut microbiome and the pre-modern human ancestor. These ancestral microbiome studies are tying together bodies, microbes, environments, and time in problematic and reductive ways that require analysis to make clear how present-day indigenous people are being embroiled in a rhetoric that values their bodies as both “windows into the past,” and “genetic storehouses” for the production of future therapeutics.

Several papers state that a goal or outcome for their research is to build a library of samples, or contribute sequencing data to an enormous database of microbial DNA, much of which is shared among research institutions and used to identify novel microorganisms from metagenomic samples. These studies are not designed to categorize the microbial populations and function within indigenous people in order to understand the specific and unique health issues of those precarious communities. These studies do not intend and do not even attempt to articulate their research as directly benefitting the communities from which they collect biological materials.

Instead, these studies make clear that the goal of their research is to build massive microbial databases to further their academic fields and develop novel therapeutics that will provide restoration of the dysbiotic western microbiome using genetic materials taken from the bodies of indigenous people, at no benefit to them.

De Filippo et al conclude their study of microbial sampling of children in Burkina Faso by writing, “the worldwide diversity of the microbiome from ancient communities … represents a goldmine for studies aimed at elucidating the role of gut microbiota on the subtle balance between health and disease and for development of novel probiotics.” When De Filippo et al write that we need to “preserv[e] this treasure of microbial diversity from ancient rural communities worldwide,” we must ask, whom is this “treasure” for? And who will benefit from the “goldmine” of microbial life in indigenous bodies?

Moreover, and perhaps most important to the larger problem of who benefits from this research, De Filippo explain in a small section at the end of their paper that they enrolled 15 healthy children from Burkina Faso. They enrolled 15 healthy children despite the “high incidence of infectious disease, including malaria and malnutrition in the area.” Despite the fact that malnutrition is not an infectious disease, but rather a moral and economic failure of global politics, this brief mention illuminates the key trouble in ancestral microbiome studies. Researchers are spending thousands of dollars to travel to “isolated” indigenous communities, collect oral/fecal samples, then analyze and compile their sequencing data into a shared database, but the communities from which they gather the raw materials of their work are dying from curable diseases.

Research to understand the ancestral state of humans and their microbial symbionts by extracting biological materials from rural indigenous people is built on colonial logics of human difference and time, deploys insidious narrative tropes related to “isolated” and “vanishing” indigenous communities to justify research, and depoliticizes the sampling practices of ancestral microbiome scientists in ways that threaten the lives and livelihoods of indigenous people. These studies are shameless in their aims to develop novel therapeutics that might aid western populations suffering from chronic autoimmune diseases by culling microbes from the bodies of people who continue to die from preventable ailments like pneumonia, malaria, diarrhea, and hunger.

By placing modern people in an ancient context, microbiome researchers are absolved of having to see the indigenous sampling populations as people living in the present, facing “modern plagues” that are not obesity and autoimmune disorders, but massive poverty, pollution, climate change, militarization, and economic displacement. This general research frame turns people into resources and the temporal collapse allows researchers to naturalize problems like malnutrition and infectious disease that takes the early lives of indigenous people and to sidestep the global politics that produce such people as “untouched” and “non-industrialized.”

This dynamic gets at the heart of problems around ancestral microbiome research—westerners may want to cultivate more gut microbial diversity, but they surely don’t want to give up filtered drinking water, antibiotics, indoor plumbing, and packaged foods. Because along with the practices that cultivate a “diverse” and “unique” gut microbial population among rural indigenous communities comes economic disinvestment, developmental neglect, and the violences of colonialism.




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