Bugs as Features

Digital metaphors for the human microbiome abets fantasies of reprogramming our guts and rebooting our systems

Popular science has been overrun in recent years with guides to the microbiome — the aggregate genetic substance of all the microorganisms living in and on our bodies. Beyond a naive understanding of bacteria as uniformly pathogenic, titles like The Microbiome Solution: A Radical New Way to Heal Your Body From the Inside Out (by Georgetown gastroenterologist Robynne Chutkan) and The Good Gut: Taking Control of Your Weight, Your Mood and Your Long-Term Health (by Stanford microbiologists Justin and Erica Sonnenberg) have popularized a conceptual turn toward recognizing bacteria as potentially beneficial. These handbooks are particularly attentive to microorganisms located in our gastrointestinal tracts as arbiters of individual wellness.

An interest in healthful bacteria is traceable to the origins of germ theory itself, at the turn of the 20th century, among pioneers like immunologist Élie Metchnikoff. Until recently, however, research into the microbiome was something of a niche focus. Now it is proliferating in several directions, and interesting findings are emerging on all fronts: Characteristic gut bacteria profiles have been noted, for instance, in conditions as diverse as colon cancer, diabetes, and the autism spectrum. Yet the persistent impulse to make these findings immediately actionable tends to render them cartoonish. Contemporary fad diets and nutraceuticals exploit an almost Zoroastrian perception of health as a function of balance between good and bad microbial elements. Associative findings are treated as causative conclusions, and easy interventions like fermented foods and probiotics come to serve as feel-good talismans for warding off the threat of chronic disease.

Contemporary fad diets exploit an almost Zoroastrian perception of health as a function of balance

Public understanding still relies heavily on simplifying metaphors for the microbiome, even as it embraces a slightly more complex understanding of microbes’ role in human health. For years, the dominant metaphor has been environmental: Peer-reviewed literature dating back to at least 1960 discusses the gut in terms of its “microbial ecology.” This rhetoric has a sound methodological basis, as environmental science techniques for analyzing biodiversity were directly transferable from the study of larger ecosystems to that of bodily surfaces. The vision of the microbiome as a natural landscape has become steadily more explicit, such that the academic and lay press now repeatedly describe the gut as like a forest or garden.

With time, this particular way of thinking about the microbiome has also become charged with the politics of conservation biology, channeling the emotional valence of lost biodiversity in the larger world. When the environmental idiom is used to describe our co-habitating bacteria, it often comes with a tone of Anthropocenic remorse, a familiar sense that humans are inclined to destroy any preexisting natural equilibrium. This tone replicates at a bodily scale the logic and guilt associated with, for example, man-made climate change and ecosystem disruption. Microbiologist and physician Martin Blaser has deployed the image of a dying forest to establish the tragic stakes of microbial depletion over time: “Ninety percent of the trees are dead, waiting for a fire to turn them to ash … what happens when ecology changes, not in a forest, but inside a person?”

As I’ve argued elsewhere, this posture of reflexive mourning tends to structure our understanding of the microbiome as fragile, its injuries irrevocable. The attitude corresponds to valuing stasis and retrospection in health-seeking behavior; it fetishizes pre-industrial bodies and habits and calls for the mindful avoidance of surgery, antibiotics, and other aggressive medical interventions wherever possible.

More recently, however, conversations about the microbiome have been infiltrated by a second set of metaphors, one rooted in the language of digitality and code. As with the ecological view, there is some scientific basis for this rhetoric, if for no other reason than microbiologists’ progressive reliance on computational sequencing methods to negotiate a vast amount of genomic data. But the digital framework for understanding the microbiome comes with its own particular emotional inflection, one that is almost diametrically opposed to the ecological alternative.

The environmental idiom for our co-habitating bacteria often comes with a tone of Anthropocenic remorse, a familiar sense that humans are inclined to destroy any preexisting natural equilibrium

A growing awareness of the enteric nervous system as a signal mediator between the microbiome and the human body has led to comparisons to data transmission — what one reviewer at Nature has termed “bacterial broadband.” Endowing the organisms that live inside our bodies  with the qualities of software lends credence and charm to the possibility of a complete system reboot. Relative to the ecological framework, indigenous microbial colonies are reconfigured from endangered species into programs that can be erased and reinstalled. Through this lens, the microbiome’s dominant quality becomes plasticity rather than fragility; with enough technical know-how, the constituents of any given gut might be fully customized to its user’s liking. Bugs, so to speak, become features.

Computational metaphors for the brain and the body have some notable shortcomings: Psychologist Robert Epstein highlights the faulty but persistently seductive idea that memory works as a kind of data storage, while writer Kristen V. Brown emphasizes the folly of recent attempts in Silicon Valley to reduce the complexity of physical processes to simple algorithms. The digital metaphor for the microbiome is vulnerable to similar criticisms. When the rhetoric is taken too literally, therapeutic practices skew toward hubris; they elide individuals’ biological and environmental idiosyncrasies, treating body parts like standard-issue hard drives primed for uploads.

But all of these digital metaphors conform with broader ideas about technology extending human control. Gut Hack, a short-form documentary released earlier this year, provides a clear example of the microbiome’s digital metaphor in operation. The film follows a synthetic biologist named Josiah Zayner as he addresses his longstanding gastrointestinal distress through a self-directed stool transplant. Zayner solicits a fecal donation from an acquaintance, takes antibiotics to sterilize his alimentary canal, checks into a hotel room, scrubs his body down, and then ingests the feces in pill form. Intercut with this narrative are short passages stressing the imprudence of this type of self-experimentation, which serve only to heighten the drama of Zayner’s daredevil heroism. He subsequently reports an improvement in his symptoms, which, alongside a genetic analysis that confirms a shift in his microbial profile, seems to indicate a successful intervention. This result in turn apparently vindicates a digital understanding of the microbiome, whose healthy “code” can be retrieved and rewritten as easily as that of any piece of software.

When the digital metaphor for the microbiome is taken too literally, therapeutic practices skew toward hubris, treating body parts like standard-issue hard drives primed for uploads

As a medical procedure, fecal microbiota transplantation (FMT) is currently FDA-approved only for recurrent or refractory infectious colitis caused by an organism called Clostridium difficile. Researchers are studying the effects of FMT, however, in a variety of other conditions (e.g. inflammatory bowel disease, metabolic syndrome) in which the microbiome has been implicated. In the absence of experimental results to the contrary, the procedure’s hypothetical applications are poised to ripple outward. While do-it-yourself FMT instructions have been available online for years among patients who fall outside conventional regulatory requirements, the emerging biohacking paradigm reframes the act of microbial self-manipulation from one of therapeutic desperation to one of deliberate exploration. It idealizes the element of transgression, of pushing past the arbitrary limits of an out-of-the-box operating system.

Digital rhetoric reinforces an abiding sense of optimism, emphasizing the potential benefits of microbial manipulation and diminishing its harms. As a self-described biohacker, Zayner promotes a larger project of taking science out of the laboratory by selling gene-editing kits to anyone who wants to buy them. The prospect of this new technology’s unrestricted use carries with it the potential for deeply felt social impacts — home-brewed pandemics, for instance, or a sort of back-alley eugenics revival — that are much more unsettling than the risks of amateur FMT. Generally accepted ethical boundaries have yet to be established for gene-editing systems, but despite this ambiguity, they’ve been assimilated readily into the biohacking agenda. We must presume that Zayner has accounted for the likelihood of recklessness, if not outright malice, within his customer base before putting these products on offer.

The search for an optimal microbiome metaphor in popular communication has its echoes in the administrative arena, as groups like the FDA struggle toward aligning emergent microbial therapies with clear regulatory precedents. Are probiotics more like supplements or drugs? Are stool transplants more like blood products or organ grafts? Persistent uncertainty about these interventions’ biological ramifications has stalled the development of consensus policy definitions, though efforts toward therapeutic implementation by corporations and individuals have certainly continued to move forward.

As the science matures and still newer therapies are put forward, more subtle and more appropriate metaphors for the microbiome may yet arise — perhaps ones that de-emphasize the boundaries of the individual body or that strike a balance between notes of frailty and resilience. For now, though, recognizing the ecological-digital binary and the potential to swing between these poles seems more productive than adhering too closely to either metaphor in isolation. Each highlights the other’s bias, and indeed their cycling might even suggest a process of communal self-correction. Holding the two frameworks in tension will ideally prevent both of their reductive moral narratives from being too readily digested.

Nitin K. Ahuja is a physician living in Philadelphia, Pennsylvania.