Designing the Microbiome: Bacterial Cultures Lab Inquiry

July 30, 2014

Microbes collected during the

Microbes collected during Kristina Ortega’s “Microbiome Association Swabbing Party.”

By Dr. Christina Agapakis, Adjunct Faculty

When it comes to bacteria, we can’t seem to make up our minds. On one hand, many people won’t leave home without their anti-bacterial hand sanitizer. On the other, probiotics — the “good bacteria” — have become so popular, they’re added to food and beverages that are otherwise devoid of nutrients. The tension signals we’re at the brink of a major change in attitude about microbes.

A new model of biology is currently emerging in research labs. With improving tools to measure and account for the teeming diversity of bacteria that live in our bodies and in our environment, the complexity of life in its ecological contexts is inspiring new questions and new understandings of living things. In a recent article, the anthropologists Heather Paxson and Stefan Helmreich frame the shift as a turn from the 20th century “age of biological control” to a model of nature “swarming with organismal operations … and full of yet-to-be explored possibility.”

For designers and artists, this model of biology provides a very different perspective, after decades in which genetic engineeringtissue engineering, and synthetic biology were the dominant scientific topics crossing over into creative realms. As biological engineers seek to design living things, artists and designers are offering a range of critical perspectives on the role of culture, politics, ethics, ecology, and aesthetics in the “age of biological control.”

As a synthetic biologist and a visiting professor in MDP/Lab, I work with the students as they explore emerging ideas from microbiology and biotechnology. Over the course of an intensive four-week “Inquiry” into the science, technology, and design of microbial systems, students develop critical design projects that reimagine our human relationship to microbes.

What sorts of questions might emerge when we are designing with microbes, for a biology that remains underdetermined and out of our control? Instead of a future where evolution is tamed by genetic engineering and where microbes always work according to spec, how do we design ways to nurture a complex and diverse ecosystem? How do we design for adaptation, robustness, and change? How will we design with biology in the future?

Xiaochen Yang's ProbioPETs in use.

Xiaochen Yang’s ProbioPETs in use.

These questions apply when designing for the relationship of humans and microbes at many scales, from the species of bacteria in probiotic foods to the structure of city wastewater infrastructure. The Bacterial Cultures Lab Inquiry in January 2014, the second synthetic biology project that I have co-taught with MDP faculty Ben Hooker, explored a range of these possibilities as students imagined products and services for a new microbial world.

Below is a small sampling of the projects by some of the students:

Neighborhood watch programs have traditionally focused on spotting human-scale intruders on the block, but Kristina Ortega proposes community monitoring at the microscopic level. The Microbiome Association organizes friends and neighbors to share probiotic starter cultures for lacto-fermented pickles or sourdough bread, helping to promote the spread of “healthy” bacteria. At “swabbing parties,” people share beers and petri dishes, bringing the invisible members of the community into view, and different houses can be scored for microbial diversity and scolded when improvement is needed. New community practices emerge when the microbial members of the community are considered, from monthly bacterial screenings to holiday celebrations designed to spread good cheer and probiotics through the neighborhood.

Satellite view of the York Boulevard Microbiome Neighborhood Association, Kristina Ortega.

Satellite view of the York Boulevard Microbiome Neighborhood Association, Kristina Ortega.


Plenty of bacteria are shared even within a single household. Xiaochen Yang’s ProbioPET focuses on the microbes shared between families and their pets. Research shows that pets significantly enhance the microbial diversity of a home, and can facilitate the exchange of microbes between family members. Yang’s idea enables that intimate bacterial exchange even when family members are far apart. Like skyping with your cat while on a business trip, The PriobioPET allows couples in long distance relationships or grandparents in other cities to share their microbiome even without shared physical space. These objects create new rituals and habits, encouraging us to think of ourselves and our relationships as shared ecosystems.

ProbioPETs, Xiaochen Yang.

ProbioPETs, Xiaochen Yang.


New awareness of the human microbiome might also change how we interact with and monitor our individual health. Imagine an app that turns the opaque functions of your internal organs into dynamic data visualizations. Tim Kim’s Fart Alarm takes Quantified Self to new heights and depths, with a “dashboard” for tracking your digestion. As your body processes a meal, the production of wastes and gas shows up on your smartphone screen in the form of fractal patterns of bacterial growth and change. With such a biological timer in your pocket, you just might be able to avoid embarrassing moments in the movie theater.

The Fart Alarm establishes communication between the gut and your phone. Image by Tim Kim.

The Fart Alarm establishes communication between the gut and your phone, Tim Kim.


Outside the realm of personal health, microbes play other important roles. Bacteria can evolve and adapt rapidly by exchanging DNA between individuals in a community. This kind of horizontal gene transfer makes it difficult to define a stable “tree of life,” another way that microbes resist control. With Social Cognitive Recombination AccessoriesZoe Padgett uses this process as a metaphor for people’s social exchanges. During an awkward silence at a party, Padgett’s invisible earpiece would pick up on the social context and deliver a phrase pulled from the Twitter stream of a celebrity like Brittney Spears or Yoko Ono. Suddenly the ice is broken, social dynamics and reshuffled, and new conversational adaptations evolve.

Consoling with Metaphor and Ambiguity with @YokoOno, using the Social Cognitive Recombination Accessory, Zoe Padgett

Consoling with Metaphor and Ambiguity with @YokoOno, using the Social Cognitive Recombination Accessory, Zoe Padgett


Mutation, recombination, and evolution can also play a role in our software ecosystems. Synthetic biology hopes to apply the logic of computer science and software engineering to biological systems; what might happen when computer systems are designed based on the logic of biology? Like Zoe Padgett, Marcus Guttenplan and Jenny Rodenhouse also based their project, Metagerminationon the concept of horizontal gene transfer. They designed “digital bacteria” that could exchange information between websites, collecting and swapping metadata to speed up the evolution of digital histories.

Metagermination Data Creatures, Jenny Rodenhouse and Marcus Guttenplan.

Metagermination Data Creatures, Jenny Rodenhouse and Marcus Guttenplan.


Together, these projects highlight an evolving uncertainty underlying biological design. Here, uncertainty doesn’t imply the potential for dangerous or dystopian outcomes of new technologies, but of instability and emergence. To design for microbes is to design for relationships, for new connections, for change, growth, and adaptation. As we invite microbes into our daily lives, encouraging greater diversity in our microbial ecosystems, we might also encourage a new diversity in how we design.


This post was edited by Anne Burdick for the Lab blog and Sarah C. Rich for the “re:Form” series in Medium.