RNA sequencing strategy provides insight into microbiomes

Gut microbiome

New RNA sequencing strategy provides insight into microbiomes

A high-throughput RNA sequencing strategy has been developed by the researchers of the University of Chicago to study the activity of gut microbiome. Tools allow researchers to understand the activity of naturally occurring microbiome in response to the real world conditions and diet.

The new equipment analyzes the transfer RNA (tRNA), a molecular Rosetta stone that translates the encoded genetic information in DNA into the protein that executes the basic biological functions. By developing a clear picture of tRNA mobility, researchers will be allowed to understand the activity of naturally occurring microbiome and to change environmental changes such as their temperature, or to change the availability of various types of nutrients.

Recently, a new study report has been published in Nature Communications that was conducted by the team of scientists led by Tao Pan;  a professor of biochemistry and molecular biology and A. Murat Eren;  an assistant professor of medicine at the University of Chicago. They diet demonstrated application of tRNA sequencing to reduce sample of the microbiome from mice that either low-fat or high-fat was fed.

The new software and computational strategy described in the study created a list of the tRNA molecules recovered from the intestinal samples, found them back in the bacteria responsible for their expression, and measured chemical modifications in the transmitted tRNA.

There is an average of eight chemical modifications in each tRNA in bacteria that can tune its function. The new high-throughput indexing and analysis strategy detects two of them, but it can also measure amounts of 0 to 100 percent revision on each site. The level of one of the modifications, called m1A, was high in microbial in the gut of rats, which was fed to high-fat food. This is the first time that scientists have seen any amendment level changes in any microbiome in tRNA.

“We did not have any prior idea of why tRNA m1A modifications actually existed or what they were doing, but seeing no change in the alterations at all in the microbial is unprecedented. There are a number of ways to examine microbial activity, but there is no way to see what is faster and gets a greater amount of data than serialization. Here we have developed a new way of reporting microbial activity through the tRNA and doing so in high productivity, said Tao Pan in a statement.”

The m1A modification helps to form certain types of proteins that may be more abundant in a high-fat diet. Researchers do not yet know whether these variations in the modification occur in response to this diet, or if they already exist and become active to promote the synthesis of these proteins.

This study is the first of a series of microbial projects from the University of Chicago funded through a grant from the Keck Foundation. Researchers have pioneered the overall use of tRNA sequencing tools and will fund continued work to make them widely available through new computing strategies. Large groups of data from the tRNA sequence can provide critical insights into the microbiomes associated with humans or the environment at a lower cost.

"The molecular and computer progresses that have emerged over the last two decades have only helped to scratch the surface of microbial life and their impact on their environment." By providing fast and reasonable insights into the core of the translational machinery, tRNA sequencing may not only become a way to gain insights into microbial responses to environmental changes Which cannot be easily measured by other means but also bring more RNA biology and RNA epigenetics to the rapidly evolving microbial field, said and A. Murat Eren in his statement.

Tao Pan and A. Murat Eren agree that there is much room for improvement in this new strategy, and hope it will happen quickly.

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Journal Reference: 

Nature Communications, 2018; 9 (1) DOI: 10.1038/s41467-018-07675-z

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