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Analytical Chemistry

Bacterial Messengers

Method encodes and decodes text messages

by Stu Borman
October 10, 2011 | A version of this story appeared in Volume 89, Issue 41

Living Cipher
Credit: Manuel Palacios
Microbe arrays like this one can encode messages about one sentence long.
Credit: Manuel Palacios
Microbe arrays like this one can encode messages about one sentence long.

Aiming to enhance the interface between chemistry, biology, and information technology, a team has developed a technique to encode information in patterns of bacteria and reveal it fluorescently.

“Our technique can potentially be used for easy-to-read biological bar coding, as a deterrent to counterfeiting, or for secret communications,” says postdoc Manuel A. Palacios of Tufts University, first author of a paper describing the approach (Proc. Natl. Acad. Sci. USA, DOI: 10.1073/pnas.1109554108). The study was carried out by Palacios, Tufts chemistry professor David R. Walt, Harvard University chemist George M. Whitesides, and coworkers.

The technique’s advantage is the use of a visible, easy-to-read output for the encoded information—the output being a pattern of fluorescent signals produced when the bacterial messengers are grown in an array. Nonbiological information has been encoded in the DNA of microorganisms before, mostly for bar coding, but expensive sequencing or other molecular biology laboratory techniques were needed to read the messages. With the new approach, all one needs to read an encoded message is a light source to excite fluorescence and a camera to record it.

The technique was conceived as part of the Defense Advanced Research Projects Agency’s (DARPA) Chemical Communications program.

Earlier, Whitesides, Walt, and coworkers developed “infofuses,” which act as infrared signal flares to send messages to remote viewers (Proc. Natl. Acad. Sci. USA, DOI: 10.1073/pnas.0902476106). Now, the group has extended that concept by developing a signaling mechanism mediated by bacteria instead of being propagated directly through space.

The technique makes use of seven strains of bacteria genetically engineered to express different fluorescent proteins. By assigning a color pair to a letter, number, or other character, the seven strains can encode 49 alphanumeric characters.

To compose a message, the sender spots on a membrane the pattern of bacterial pairs that spells the information. At the decoding stage, the recipient stamps the message-containing membrane into a growth medium, induces fluorescence expression, and reads the pattern of fluorescent dots visually according to the agreed-upon color code. Walt and coworkers call the technique “SPAM” (Steganography by Printed Arrays of Microbes).

One could argue that there is no preexisting problem that the SPAM technique solves, because there are already many nonchemical ways to transmit secret or encoded information. In response, Walt explains that SPAM meets DARPA’s requirements for a nonelectronic encryption system and has advantages over current encoding systems. Notable among these are its many layers of security, such as the code, the growth medium, the timing needed to express the signals (which can be made variable), and the ability to encode multiple messages in the same array (by using bacteria resistant to different antibiotics, for example).Computational biologist Masanori Arita of the University of Tokyo says SPAM’s current 49-character repertoire is somewhat limiting. Nevertheless, he says, the technique is “an elegant way to visualize human-encoded information and brings the world of biotechnology and computation much closer.”


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