Researchers from the Wyss Institute at Harvard University and Harvard Medical School (HMS) have created a genetic-signal transmission system in the gut of a mouse. The system records the molecular signal occurring with the over 1,000 species of bacteria that live in the human gut, also known as the gut's microbiome. This new development takes microbiome research one step closer to creating a synthetic biome that can be programmed to perform specific functions in the body.

Source: Wyss Institute at Harvard University

"In order to improve human health through engineered gut bacteria, we need to start figuring out how to make the bacteria communicate," said Suhyun Kim, a graduate student in the lab of Pamela Silver at the Wyss Institute and HMS, who is the first author of the paper. "We want to make sure that, as engineered probiotics develop, we have the means to coordinate and control them in harmony."

The team used “quorum sensing,” a naturally occurring phenomenon that occurs when bacteria sends and receives signal molecules that show overall density, and regulates expression of genes in group activities.

One type of quorum sensing is called acyl-homoserine lactone (acyl-HSL). Acyl-HSL has never been observed before in the body. The team repurposed acyl-HSL to the signaling system to create a bacterial information transfer system by using genetic engineering.

The team introduced two different genetic circuits, a signaler and a responder, to two different E. Coli colonies in a mouse biome. The signaler contains one copy of the "luxI" gene that is turned on by the anhydrotetracycline (ATC) molecule. The signaler produces the quantum sensing molecule in the biome. The responder is activated when the signaller bonds to it, the "cro" gene produces "Cro," which turns on the “memory element” in the responder.

The memory element of this process produces two genes: LacZ and another copy of Cro. LacZ causes the bacterium to turn blue if placed on a special agar. This produces a color change indicator that the signal molecule has been received. The extra copy of Cro creates a positive feedback loop that keeps the memory element of the process is activated.

This process proves that the system can work in vitro in E. coli and S. Typhimurium bacteria. The team placed the signaler and the responders in E. coli bacteria in mice. They then had the mice drink ATC-laced water for two days, after which the excrement of the mice showed that the process was working.

"It was exciting and promising that our system, with single copy-based circuits, can create functional communication in the mouse gut," explained Kim. "Traditional genetic engineering introduces multiple copies of a gene of interest into the bacterial genome via plasmids, which places a high metabolic burden on the engineered bacteria and causes them to be easily outcompeted by other bacteria in the host."

After the successful E. coli experiment, the team tested the system with an S. Typhimurium signaler and an E. coli responder. This was also a successful test of the system.

The team’s next step is to continue the study on more types of bacteria and eventually testing it on human participants.

"Ultimately, we aim to create a synthetic microbiome with completely or mostly engineered bacteria species in our gut, each of which has a specialized function (e.g., detecting and curing disease, creating beneficial molecules, improving digestion, etc.) but also communicates with the others to ensure that they are all balanced for optimal human health," said corresponding author Pamela Silver.

"The microbiome is the next frontier in medicine as well as wellness. Devising new technologies to engineer intestinal microbes for the better while appreciating that they function as part of a complex community, as was done here, represents a major step forward in this direction," said Wyss founding director Donald Ingber, M.D., Ph.D.

The paper on this research was published in ACS Synthetic Biology journal.