A simulated robot with bacterial brain

Models how bacteria might affect the mind (bacteria that act like tigers?); applications may include treating mental and physical illnesses, agriculture, and remediating oil spills
July 28, 2015

Computational Simulation of microbiome-host interactions. (A) A basic gene circuit forms the core of all simulated gene network behavior. (B) Green fluorescent protein (GFP, shown as a green dot) from this circuit is conceptualized to be detected by an onboard miniature, epifluorescent microscope (EFM). (C) A computational simulation of microbiome GFP production based upon an analytical model for the circuit in (A). In a built system, this protein fluorescence signal would be the light detected by the EFM. (D) The conceptualized robot uses onboard electronics to convert the measured light signals into electrical (voltage) signals. (E) Voltage signals meeting specific criteria activate pre-programmed robot motion subroutines. (F) The resulting emergent behavior potentially leads a robot to a carbon fuel depot. Here, robot behavior resulting from a simulation of the circuit in (A) is shown. The robot was programmed with motion subroutines that activate to seek arabinose (synthesized from glucose, orange square) depots following receipt of lactose (cyan triangles). (credit: Keith C. Heyde & Warren C. Ruder/Scientific Reports)

Virginia Tech scientist Warren Ruder, an assistant professor of biological systems engineering, has created an in silico (computer-simulated) model of a biomimetic robot controlled by a bacterial brain.

The study was inspired by real-world experiments where the mating behavior of fruit flies was manipulated using bacteria, and in which mice exhibited signs of lower stress when implanted with probiotics (“healthy” bacteria).

A math model of microbiome-controlled behavior

The deeper motivation for the study was to understand how the microbiome (the bacteria in the human body, thought to number ten times more than human cells) might influence human behavior. For example, some studies show that the gut microbiome influences human eating behavior and dietary choices to favor the survival of the bacteria. (See Do gut bacteria control your mind? for example.)

As explained in an open-access paper published recently in Scientific Reports, Ruder’s study revealed unique decision-making behavior by a bacteria-robot system by coupling and computationally simulating equations that describe three distinct elements: engineered gene circuits in E. coli, microfluid bioreactors, and robot movement.

In the mathematical model, the theoretical robot was equipped with sensors and a miniature microscope to measure the color. The hypothetical robot was designed to read E. coli bacterial gene expression levels (how much protein is created by specific genes), using light sensors in miniature microscopes. The bacteria turned green or red, depending on what they ate.

Bacteria that act like tigers?

Interestingly, the bacteria in the model began to approach a fuel source with “stalk-pause-strike” behavior, characteristic of predators.

Ruder’s modeling study also demonstrates that these sorts of biosynthetic experiments could be done in the future with a minimal amount of funds, opening up the field to a much larger pool of researchers.

Understanding the biochemical sensing between organisms could have far reaching implications in ecology, biology, and robotics, Ruder suggests.

In agriculture, bacteria-robot model systems could enable robust studies that explore the interactions between soil bacteria and livestock. In healthcare, further understanding of bacteria’s role in controlling gut physiology could lead to bacteria-based prescriptions (probiotics) to treat mental and physical illnesses. Ruder also envisions droids that could execute tasks such as deploying bacteria to remediate oil spills.

Bacteria effects on behavior

The findings also add to the ever-growing body of research about bacteria in the human body that are thought to regulate health and mood, and especially the theory that bacteria also affect behavior.

“We hope to help democratize the field of synthetic biology for students and researchers all over the world with this model,” said Ruder. “In the future, rudimentary robots and E. coli that are already commonly used separately in classrooms could be linked with this model to teach students from elementary school through the Ph.D.-level about bacterial relationships with other organisms.”

Ruder plans next to create a real-world version of the experiment, creating mobile robots with bioreactors on board that harbor living colonies of bacteria that direct the robot’s behavior.

The Air Force Office of Scientific Research funded the mathematical modeling of gene circuitry in E. coli, and the Virginia Tech Student Engineers’ Council has provided funding to move these models and resulting mobile robots into the classroom as teaching tools.

Virginia Tech | Scientist shows bacteria could control robots

Abstract of Exploring Host-Microbiome Interactions using an in Silico Model of Biomimetic Robots and Engineered Living Cells

The microbiome’s underlying dynamics play an important role in regulating the behavior and health of its host. In order to explore the details of these interactions, we created anin silico model of a living microbiome, engineered with synthetic biology, that interfaces with a biomimetic, robotic host. By analytically modeling and computationally simulating engineered gene networks in these commensal communities, we reproduced complex behaviors in the host. We observed that robot movements depended upon programmed biochemical network dynamics within the microbiome. These results illustrate the model’s potential utility as a tool for exploring inter-kingdom ecological relationships. These systems could impact fields ranging from synthetic biology and ecology to biophysics and medicine.