Researchers at St Petersburg University have created a new algorithm for the analysis of metagenomes — sets of genomes of large communities of microorganisms that live, for example, in soil, water or the intestines of animals and humans. The new tool helped to find out that today only half of the wide variety of intestinal bacteria living in people’s bodies are known.
One of the important tasks of bioinformatics is to restore the sequence of the genome — it contains the hereditary information of any living being. The solution of this difficult problem consists of two stages: sequencing («cutting» the DNA molecule into small «pieces» and reading each of them separately); and assembling, when mathematical algorithms are used to reconstruct the genome from fragments (reads). The longer and more accurate the reads are at the time of sequencing, the more efficiently the algorithms of assembling work, which means you can learn more about the host of the genome — the animal, the plant or the bacteria. However, the creation of long reads is more expensive, so researchers often prefer short fragments.
The results of the study are published in the journal Cell Systems.
Today, scientists are able to work not only with a single genome, but also with their aggregates — metagenomes. This can be the genetic material of a large community of bacteria that lives in soil samples, in water at the bottom of the oceans, in sewage and even in the human intestine. The new algorithm allows to more effectively study this genetic assortment. It has been developed by the authors of the article in Cell Systems: Anton Bankevich — Junior Research Associate of St Petersburg University; and Pavel Pevzner — Head of the Laboratory «Centre for Algorithmic Biotechnology» of the Institute of Translational Biomedicine of St Petersburg University.
Researchers at the University of St Petersburg were the first in the world to offer research on rare bacteria by analysing the results of sequencing of two technologies at once: Illumina, which makes it possible to obtain short DNA fragments, and TruSeq Synthetic Long Reads (TSLR), which helps to restore longer sections of the genome. Bioinformatics researchers use various mathematical methods to search for the regions where both short and long DNA coincide. It makes it possible to understand which reads came from bacteria highly metagene in the metagenome, and which are rare.
Anton Bankevich said that «Unfortunately, we do not know exactly to which fragments of the genome each bacteria belongs. However, the new algorithm helps us predict the size of the "white spot" — an unexplored area of the metagenomeh. This information allows you to see the full scale of the diversity of the bacterial community, and therefore to save a lot of research funds. According to our calculations, the total length of the genomes of bacteria in the human intestine is 1.3 billion nucleotides, and the length of the genomes of intestinal bacteria, which today has been restored by researchers, is only 656 million. This means that we know only about 50% of the microorganisms that live in our stomachs».
Most likely, the researcher notes, the half that is known is the most important one. Nevertheless, scientists around the world continue to study various metagenomes and look for unknown types of bacteria in them. Such findings may have interesting properties eand, in the future, become the basis for new types of antibiotics, pesticides or, for example, help in the creation of disease-resistant vegetables and fruits. In addition, such studies will help us to learn more about various diseases of the gastrointestinal tract — from elementary disorders of the stomach to Crohn’s disease.
Recently, scientists have proposed to consider human microbiota — a community of bacteria living in symbiosis with the human body — one of the organs of the body along with the heart and lungs. Its diseases are as dangerous as diseases of other organs, and are often associated with a decrease in the diversity of bacteria. The method proposed in the article makes it possible to measure and observe how the state of the microbiota changes, which means that it can help in its treatment.