Bioinformatics – Medicine

Alexey Shabelsky, RosnaukaA team of Russian scientists led by Professor Pavel Pevsner managed to become world leaders determining trends in the development of bioinformatic software.

As part of the work on the government megagrant, Pevsner, as a full-time employee of the American University, created a laboratory in St. Petersburg to study the properties of the bacterial genome.

Employees of the Center for Algorithmic Biology of St. Petersburg State University told the correspondent "Rosnauka.ru "why it is so important to study the genetic composition of the bacteria around us and what contribution St. Petersburg scientists have made to these studies.

There are many times more bacterial cells in the human body than his own. The totality of human microorganisms makes up the microbiota, which largely determines its vital activity. Without the participation of bacteria, neither digestion, nor immunity, nor many other processes will work properly. The overwhelming majority of our inseparable neighbors are useful to the body, although even a healthy person has pathogenic representatives of the microflora. In relation to beneficial bacteria, there are few of them, and normally this proportion should remain constant. Violation of this balance leads to serious diseases.

However, even beneficial bacteria can, under certain conditions, degenerate into pathogenic strains. E. coli (Esherichia coli), without which we cannot digest food, is capable of forming pathogenic forms that are harmful to humans as a result of mutations. This transformation occurs due to spontaneous changes in the bacterial genome. If you fix them and understand what they come from, then you can fight the pathogenic degeneration of the microflora. Having found out the peculiarities of the genome of such modified bacteria, it is possible to purposefully disrupt its work and cause the death of pathogenic microorganisms or, at least, interrupt the process of their reproduction.

This is one of the most important tasks of bioinformatics. Today's technologies cannot read the entire DNA molecule from beginning to end – it is too long for them. Therefore, scientists have to act like this: having isolated DNA from a cell, they split it into many short segments of 200-300 nucleotides in length, and then decipher the sequences of nucleotide pairs in them. Next, the researchers face the question: how to put them together correctly in order to restore the original DNA molecule, which contains tens of millions of nucleotides. This task is solved with the help of special bioinformatic programs.

The achievements of modern bioinformatics allow for fast and accurate genomic analyses of microbiota. Today, advanced medical clinics are beginning to use it, and in world practice it is becoming the norm. An important task of bionformatics scientists is to facilitate the work of a doctor as much as possible, to create effective, but at the same time as simple programs for him. So far, doctors are just beginning to develop in this area. Nevertheless, to date there are already several high-profile success stories of the application of bioinformatics achievements in medicine.

The use of a bioinformatic approach allowed European doctors to defeat an outbreak of fatal diseases caused by a rare mutagenic strain of E. coli in 2011. It turned out that this type of bacteria is not susceptible to the action of antibiotics known at that time. Specialists needed to quickly understand how to treat the disease caused by the degenerated microflora. To do this, you need to know what has changed in the genome of the rod and why it has become pathogenic. Sequenced genomic manipulations made it possible to answer this question in two weeks. DNA was extracted from the pathogenic Esherihia coli, its primary structure was determined and changes in its genome were revealed by comparative analysis methods. Based on the data obtained, antibiotics effective for treatment were proposed. The whole process took specialists about three weeks, although a little earlier it would have taken from two to three months.

It is known that almost all autistic children have stomach and digestive problems. It turned out that their microbiota is very different from the microbiota of a healthy person – there are significantly fewer benign bacteria and bright representatives of pathogenic flora are present in large quantities. Now there are big discussions about what is primary: an increased number of pathogenic microorganisms that produce such an amount of toxins that enter the brain and change the program of its work? Or vice versa – a violation of the functioning of the brain causes changes in the body, and there are more pathogenic bacteria in it? This is very important to understand: if it turns out that autism occurs due to a large number of toxins, then by restoring the normal composition of the microbiota in the child's body, scientists will be able to treat this ailment.

Today it is unequivocally established that various diseases lead to changes in the human microbiota. There are serious studies that have shown that the same microorganism is always present in human genomic DNA isolated from cells obtained by biopsy of a rectal cancer tumor. A similar question arises: what is primary − the formation of a tumor or the colonization of this microbe into the cells? Scientists can't give an answer to this question yet.

A couple of years ago, an article was published in the journal Nature, which described an amazing experiment. He looked like this. There were two twins, one thin and the other fat. Microbiota samples were taken from both of them. (This is a painless, simple and cheap method of analysis. That is why there is a great interest in this issue now: if you find a connection between the composition of the microbiota and the disease, it is easier to take a stool analysis than, for example, a puncture. In the future, this should be an excellent way of cheap and painless diagnosis.) After that, identical mice were fed this microbiota. Those mice that received microorganisms from a thin twin remained in the same shape or lost weight, and those who got bacteria from a fat relative became fat over time. Then the scientists went even further: they took a fat mouse and put it in a cage with thin brothers. It is known that the feces of a neighbor can get into the food of rodents, so the microbiota of a fat mouse will sooner or later end up in the body of neighbors. As a result, after a while, all the mice in the cage became fat. It turned out that they were literally "infected" with obesity. Of course, such experiments have not been carried out on people because of the ethical aspect, but an inquisitive reader can find a large number of articles in which enthusiastic scientists put such experiments on themselves. They changed their diet so that the composition of their microbiota changed. The results exceeded all the wildest expectations: the experimenters managed to lose a lot of weight.

It will differ in composition: these may be the same microorganisms, but in different proportions. This year, an article was published in which for the first time it is clearly shown that a person can be identified by his microbiota. It turned out that even identical twins have an individual microbiota. The data of such an analysis of the human microbiome are relevant for at least a year. This discovery has excited the scientific community – after all, it will allow, in principle, to identify a person's identity by the DNA of his microbiota. In general, the interest of criminology in genomic research has increased significantly in recent years. This approach helps in solving problems such as the identification of remains in disasters. There were methods for solving them before, but with the use of new technologies, their accuracy has increased by orders of magnitude.

They compete for food sources and therefore they need to get rid of unnecessary neighbors, releasing toxins into the environment, i.e. antibiotics. A huge amount of antimicrobial drugs is consumed in the world, but microorganisms develop quickly and easily adapt to new influences. Scientists are constantly creating new drugs to combat such resistant strains. However, these new antibiotics are not really new – they are derivatives of previously known substances, with a slightly modified structure." Although, according to Lapidus, the possibility of treating them remains, but in a huge number of cases they do not help at all, since they do not represent anything fundamentally new. Doctors today have a great need for fundamentally different antibiotics. Scientists are looking for applicants from the world of microorganisms that can produce such substances using bioinformatic methods.

International programs for the study of the human microbiota began a long time ago, in Russia this movement is noticeably lagging behind. Alla Lapidus believes that if a person gets sick, then ideally it would be necessary to study his genome and microbiota in a complex. The composition of the microbiota will necessarily speak about the health or ill health of the patient. As soon as databases appear in the world in which it will be possible to trace the connection of the disease with changes in the microbiota, this will be an excellent diagnosis. Biotechnologists are working on the creation of such bases. To do this, you need to make a lot of samples, analyze a large number of people. Conducting such a large-scale sequel requires substantial cash injections. Therefore, these studies should be supported by the state program. 

It was created at St. Petersburg University along with other large laboratories and centers that have opened over the past two years. The work of the research team is led by Professor Pavel Arkadievich Pevsner of the University of California at San Diego. Initially, the Laboratory of algorithmic Biology was established at the Academic University in 2011 as part of the first wave government megagrant. During the work on the megagrant, scientists have conducted large-scale bioinformatic research: to date, they have analyzed terabytes of data.

Pavel Pevsner: "SPAdes, a product created in our laboratory, is one of the few Russian scientific developments that has managed to become a brand and one of the most popular genomic assemblers in the world. His fame is growing rapidly: the article about SPAdes was published only three years ago, but 200 references have already been made to it in the world scientific press in 2015 alone. In fact, there are no other products from Russia that are so popular in bioinformatics right now.

I would like to note that all this was done as part of the work on the government megagrant. Before the megagrant, there was not a single team in Russia that would deal with this issue. After the completion of the project, we managed to create a team that successfully competes with leading Western laboratories."

In 2015, the center's work will focus on ten biomedical projects in the field of genomics, immunoinformatics and antibiotic research. The center's employees see as their main goal the well-established release of bionformatic software for thousands of biomedical laboratories. Three years ago, as part of the megagrant, they created a genomic data collector that collects the chromosome back after it has been sequenced. The program was named SPAdes (Saint-Petersburg assembler), it has received worldwide recognition from bioinformatics scientists, and SPAdes is one of the best software for working with the genome of microorganisms. To date, the SPAdes genomic assembler has already been installed in 1,500 laboratories around the world. 

Everything was complicated by the fact that 90% of microorganisms known to scientists are not cultivated, that is, they do not grow on artificial nutrient media. With the development of modern bioinformatics methods, it has become possible to make do for sequencing with the amount of DNA contained in a single cell of a microorganism. A team of scientists led by Pavel Pevsner managed to ensure that the SPAdes assembler works well with such data. The laboratory staff has created a universal platform in the form of an assembler, on the basis of which it is possible to develop software for solving a number of related tasks. Scientists, for example, were able to teach the genome collector to read DNA fragments that are obtained in different ways. To do this, we had to develop various sequencing technologies.

Anton Korobeynikov, head of the genomic assembly department: "We spend a lot of effort to make SPAdes a universal means of work, convenient for the end user."

"In parallel with the development of the assembler itself, the laboratory was developing various utilities designed to solve related tasks," Korobeynikov says. – For example, the QUAST utility helps bioinformatics compare and visualize the results of assemblers designed for different purposes. This is important for the end users of the product when choosing a program to analyze their data."

The assembler creators have serious growth plans: the release of separate assemblers for RNA – rnaSPAdes, for complex diploid genomes – dipSPAdes, metaSPAdes for metagenomes.

The assembler functionality is constantly improving. The creators want to expand the possibility of using assembler to assemble genome data of organisms more complex than bacteria, for example, fungi. Their DNA is more complexly organized, and additional efforts are needed to sequence it.

The achievements of the laboratory staff, the improvement of the methods of the genomic assembler can find their application not only in microbiome research, but also in a number of related fields.

To improve quantitative methods for the analysis of close genomes. 

To develop and develop a technique for sequencing single DNA molecules in real time – SMRT.  

Create applications for analyzing the cancer genome and searching for new antibiotics.

A person's life is inextricably linked with his microbiome. Without thoroughly studying the features and mechanisms of its work, the laws by which it exists, it will hardly be possible to talk about some kind of full-fledged therapy of human diseases. The achievements of today's bioinformatics help physicians to understand and take a different look at the origin and treatment of many diseases. It is gratifying that the Russian scientific School of Bioinformatics under the leadership of Pavel Arkadyevich Pevsner is at the forefront of these studies.

The author thanks for the great help in the preparation of the material the staff of the Central Bank of St. Petersburg State University: Alla Lapidus, Anton Korobeynikov and Elena Strelnikova.

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11.08.2015