The colonized microbiome

If you were to take Atlas Biomed's gut microbiome test, you would be presented with the usual results that come from these DTC test kits such as a score of your microbiome's diversity and the identification of your gut's bacterial residents. But you would also be given insight into your microbiome's "ancestry" and "nationality". The company claims to offer you information on "which nationality, tribe or ethnic group your microbes have the most in common"... but what type of research is this based on? And what are the implications of this?

Mapping The Microbiome
in Space and Time

A subfield that is common in microbiome research is that of the biological consequences of a "Western" or "industrialized" lifestyle and diet (typically including antibiotic exposure, hygiene practices, diet heavy in refined carbohydrates), often compared against a supposed healthier, ancestral microbiome.

Such a premise has resulted in numerous studies that seek out rural, subsistence-based Indigenous communities to sequence members' microbiomes. The most commonly investigated groups include the Hadza in Tanzania and the Yanomami, Matses, and Tunapuco in South America. The introductions and conclusions of such papers often describe how the authors understand these communities as reliant on "traditional", subsistence lifestyles unaffected by urban, industrialized processes. When the microbiomes from these individuals are sequenced, the researchers determine that any differences in composition and diversity are indicative of an ideal, ancestral state that differs, in an implicitly positive way, from the results of urban, industrialized microbiomes.

If we look to ancestral microbiome research, these trends become even more apparent. For example, one study conducted shotgun metagenomic sequencing of eight paleo-fecal samples from southwestern US and Mexico, dated to 1,000-2,000 years old. They found similar composition and abundances between microbiomes of this sample and contemporary non-industrial samples from communities in Fijians, Tanzania (Hadza), Peru, Madagascar, and Mexico, with a higher abundance of certain functional genes in non-industrial and paleo samples (ex. genes for digestion of complex carbohydrates). Perhaps even more apparent is this study which conducted shotgun metagenomic sequencing of 14 “feces-containing sediment” samples from a Spanish site occupied by Homo neanderthalensis between 60-45,000 years ago. The bacterial compositional profile of these ancient samples “tend to cluster closer to Tunapuco and Matses, resembling more the 'ancestral' human gut microbiome of rural agriculturalists and hunter-gatherers than the urban western gut microbiome” . The authors of this paper conclude that there is a “core human gut microbiome” similar between H. neanderthalensis and H. sapiens sapiens that predates their evolutionary split.

This direction of research therefore seems determined to characterize and trace the evolution of the "ancestral" microbiome through industrialization through the conflation of paleo samples and extant communities, describing the loss of microbiome species and diversity as a negative hallmark that sets apart the ancestral from the industrial.

Salvage Microbiomics and Microbiomic Purity

This direction of research therefore seems determined to characterize and trace the evolution of the "ancestral" microbiome through industrialization via a conflation of paleo samples and extant communities, describing the loss of microbiome species and diversity as a negative hallmark that sets apart the ancestral from the industrial. The premise of such research is that by understanding ancestral states, modern medicine can attempt interventions to revert the chronic and autoimmune disease plagued Western, industrialized body to an idealized state of wellness.

Scholars of anthropology and science and technology studies have written on the impacts of such research. Stephanie Maroney (2017) writes,

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.

Amber Benezra (2020) describes such work as exhibiting "salvage microbiomics", that "wants to save valuable, vanishing microbes from modernization without acknowledging the research’s own embeddedness in technoscientific systems responsible for changes in microbial populations." (883).

These works are also based on assumptions of purity and isolation that supposedly characterize these communities, when in reality, such assumptions are obfuscations - "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." (Maroney 2017). Maroney (2017) further writes that "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. 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.”

Race, the Ghost Variable

Reflecting on ancestral microbiome research unveils a key assumption - that of fundamental biological differences between microbiomes and bodies that occupy different spaces. These differences become conflated with a variety of overlapping, nebulous constructed categories such as "ethnicity", "ancestry", "geography"/"environment". At the heart of these categories lies the ghost variable of race, which Benezra (2020) argues is "an operational concept in microbiome science [that] has a ghostly presence, one that is there but not there, hiding in shadows and jumping out when least expected." (879).

Benezra (2020) argues that the indefinite category of "traditional" communities "becomes racially coded to mean indigenous, undeveloped, and not-white" in contrast to the more defined and opposite category of "industrialized" (882). The direct contrast of these two constructed categories of microbiomes establish a biological justification of othering, the implications of which are serious - "without careful unpacking and recognition of colonizing scientific histories, microbiomics can racialize and discriminate. Conceiving of indigenous people as primordial, barbaric, and undeveloped has long been adriving justification for colonization, enslavement, and genocide." (883).

Conclusions

How might ancestral microbiome research be conducted more ethically?

Benezra (2020) writes that "as long as clinical research sees categories of race as preformed and rigid, and social/biological effects as separate and exclusive, the biomedical knowledge produced will incorporate these binary reifications." (891). She calls for dynamic collaborations between the biological and social sciences to develop a space of understanding microbiomes as biosocial relationships rather than separate biological and social perspectives (891).

She further describes an approach "that requires microbiome researchers to: attend to the current predicaments of research participants, support meaningful infrastructural changes, and remain alert to possible commercial exploitation" (884). One such study was conducted by molecular and sociocultural anthropologists from the University of Oklahoma, in which the gut microbiomes from individuals of the Cheyenne and Arapaho tribes were sequenced with the intention to understand "gut microbiome–associated complex diseases that are also common health disparities among American Indians" with a commitment to engage "in long-term relationships of mutual benefit and concern, trust, and understanding with the participants" (884-885).

references

Benezra, Amber. 2020. “Race in the Microbiome.” Science, Technology, & Human Values, March 18, 2020: 0162243920911998. https://doi.org/10.1177/0162243920911998.