RNA sequencing offers novel insights into the microbiome

Researchers at the University of Chicago have come up with a revolutionary strategy for studying the activity of the gut microbiome – using high-throughput sequencing of tRNA.

The microbiome - an illustration by Alpha Tauri 3D Graphics

Alpha Tauri 3D Graphics | Shutterstock

By helping scientists to understand how tRNA changes dynamically within microbiomes, the novel sequencing strategy will provide much better insight into how microbiomes found in nature react to environmental changes such as temperature variation or changes in nutrient availability.

The work is the first of several projects from UChicago, funded by the Keck Foundation, that focus on microbiomes.

Microbiomes are an area of intensive research today, because of their fundamental and wide-ranging role in health and disease.

The team, led by Professors Tao Pan and A. Murat Eren, developed new tools aimed at studying transfer RNA (tRNA) in mouse gut microbiomes. The current study reported how tRNA sequencing was applied to samples from the gut microbiome of mice who were on either a high-fat or low-fat diet.

It used newly developed software and computational tools to generate a library of tRNA molecules from the mouse gut samples.

The bacteria from which these tRNA molecules came were then identified. Finally, certain post-transcriptional modifications that occurred in the tRNA were detected and measured.

Dr. Pan was responsible for developing the tRNA sequencing tools, while Eren worked on the computational platforms that are intended to make these tools more generally available.

tRNA sequencing is an invaluable tool for obtaining high volumes of data in a cost-effective manner, to allow deeper exploration of the activity of microbiomes found in humans or in their surroundings.

Bacterial tRNA molecules are fine-tuned for their specific function by introducing post-transcriptional modifications, of which there are on average eight per tRNA molecule.

The tools used in this project are capable of detecting two modifications in a high-throughput sequencing and analysis workflow. Moreover, it can scale the degree to which this modification is present on a scale of 0 to 100 at each of the sites modified.

One of the modifications is called m1A and was found to be increased in the gut microbiomes of mice on a high-fat diet. This is a historical discovery, marking the very first time that such changes have been able to be detected at the level of modification of tRNA, in any microbiome whatever.

The scientists admit that they do not know what the presence of the m1A modifications actually means to the microbiome. In a sense, they are tracing the biological process backward to discover the significance of such modifications.

It is known that m1A enables the synthesis of some proteins that are sometimes present at higher levels in the guts of mice fed with a high-fat diet. However, it is not clear if the differences detected in the levels of the m1A modification are part of the mouse reaction to this diet, or if the already existing modification was merely activated to increase the protein production.

Over the last twenty years, many developments have occurred in molecular technology and computation. Despite this, the researchers comment that these advances have only brought us superficial knowledge of microbial life processes and how they interact with their environment.

The benefit of the new tRNA sequencing technology is its ability to provide a rapid as well as a relatively low-cost method of exploring how translation works at its core.

This could potentially yield much more insight into how microbes react following small changes in the environment, especially those that are difficult to assess by traditional methods.

In addition, the use of these tools brings greater knowledge of RNA structure and function, as well as of epigenetic changes in RNA, into the fast-expanding territory of microbiome studies.

The authors look forward to a more extensive and rapid development of the tRNA sequencing strategy they have pioneered.

There are a number of ways to examine microbiome activities, but nothing is faster and gets you more volume of data than sequencing. Here we have developed a new method that reports activity of the microbiome through tRNA and does so at high throughput. That's really the value."

Professor Tao Pan, Lead Researcher

The study was published today in Nature Communications.

Dr. Liji Thomas

Written by

Dr. Liji Thomas

Dr. Liji Thomas is an OB-GYN, who graduated from the Government Medical College, University of Calicut, Kerala, in 2001. Liji practiced as a full-time consultant in obstetrics/gynecology in a private hospital for a few years following her graduation. She has counseled hundreds of patients facing issues from pregnancy-related problems and infertility, and has been in charge of over 2,000 deliveries, striving always to achieve a normal delivery rather than operative.


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