A research team from the University of Chicago has created a new computational high-throughput RNA sequencing strategy that will provide insights into the activity of gut microbiome like never before.
The researchers specifically looked at transfer RNA (tRNA), which translate the genetic information encoded in DNA into proteins that perform basic biological functions. A better understanding of how tRNA function will enable scientists to gain insights into the activity of naturally occurring microbiomes and study their reactions to environmental changes like varying temperatures or changing availability of nutrients.
In the study, the researchers applied their direct tRNA sequencing approach to gut microbiome samples of mice that were fed either a low fat or a high fat diet. The new technique enables them to recover sequences, abundance profiles and post-transcriptional modification.
With the new strategy, the scientists can develop a catalog of tRNA molecules from the gut samples and ultimately trace them back to the specific bacteria responsible for their expression. They can also measure chemical modifications in tRNA that take place following transcription.
An individual tRNA has an average of eight chemical modifications that can determine its function in bacteria. In the new high-throughput sequencing technique, the researchers can detect two of the eight modifications, while also measuring the modification on a scale of zero to 100 percent at each targeted site.
In the study, they found that the level of one of the modifications—m1A—was higher in the gut microbiome of mice that were fed the high fat diet. This helps researchers synthesize certain types of proteins that could be more abundant in high fat diets.
“We were working backwards,” Tao Pan, PhD, professor of biochemistry and molecular biology at the University of Chicago, said in a statement. “We had no preconceived notion of why the m1A tRNA modifications were actually there or what they were doing, but to see any modification change at all in the microbiome is unprecedented.”
However, the researchers do not yet know whether the modification differences occur in response to the specific diet or if they are already present in the mice and are activated to enhance the synthesis of those proteins.
The study represents the first project in a series of studies on microbiome projects conducted by the University of Chicago and funded by a grant from the Keck Foundation. The grant will fund continuously work to make the tRNA sequencing tools widely accessible through new computational strategies, which could provide new insights into microbiomes associated with humans or the environment at a low-cost.
“The molecular and computational advances that have emerged during the last two decades have only helped us scratch the surface of microbial life and their influence on their surroundings,” A. Murat Eren, PhD, an assistant professor of medicine at the University of Chicago, said in a statement. “By providing quick and affordable insights into the core of the translational machinery, tRNA sequencing may become not only a way to gain insights into microbial responses to subtle environmental changes that can’t be easily measured by other means, but also bring more RNA biology and RNA epigenetics into the rapidly developing field of the microbiome.”
The study was published in Nature Communications.
