Day: 24 July 2018
Stanislav Smatana develops software for analysis of gastrointestinal microbiota. He received support from Brno for his research
Stanislav Smatana received the prestigious Brno PhD Talent Award. He is involved in the development of a platform for analysis of bacteria from the intestines and the use of IT tools in medicine as part of his doctoral research at the Faculty of Information Technology. He claims that unknown bacteria can be approached as "big data" whose thorough analysis will help us understand chronic diseases or drug functionality.
According to Stanislav Smatana from FIT BUT, there is an entire world in our intestines that we do not know much about yet. Despite being so unexplored, it seems that it can affect everything from our development to onset of various diseases. "About six years ago it was discovered that our colon contains far more bacteria than previously thought. The main issue was the fact that we have been unable to observe these bacteria in laboratory conditions. That is because once you remove them from the intestine, they must be cultivated and a large number of bacteria will perish in the process. Some articles report that 70 percent of bacteria will perish during cultivation, according to other articles, the number may be as high as 90 percent," Smatana pointed out.
However, researchers gradually came up with technologies which allowed us to obtain intestinal bacteria DNA without the need of their cultivation. "We already have methods we can use to collect the DNA of all bacteria in the sample and load it straight into a computer. There is no need to cultivate anymore. However, the problem that arises is that we take all the DNA without knowing what bacteria or where it comes from. We end up with a great amount of data we know nothing about," added Smatana.
Researchers' computers thus contain thousands of lines of letters which cannot be analysed by conventional methods. "And this is where information technology comes to the picture. Our main task is to develop a software that can sort such an amount of data in some way. Just determining what species of bacteria are there is really complicated because we can only identify a fraction of them," said the young doctoral student, adding that the size of a single sample is in the hundreds of gigabytes.
Another issue the experts face is modelling the ideal microbiome, i.e. our intestinal microbiota. "Microbiome helps us in a number of ways. It produces a huge amounts of enzymes, which make digestion easier. A number of drugs also rely on its work. Therefore it appears that the overall composition and balance of microbiome is important. That is a very delicate ecosystem and we need to get the overall picture regarding its workings. But the issue is how to predict something based on such amount of data," Smatana pointed out.
Ideally, in the future, experts should be able to remove a sample of bacteria from the intestines, analyse them using a computer and recommend the most appropriate diet or medication. In the first phase of his research, Stanislav Smatana focused on finding which of the available tools are best suited for analysis and how to combine them to process large amounts of data. "Currently, I am researching and attempting to implement methods that combine more information together. We have data that tells us what is in the intestine, but they do not say anything about what is going on in there. That is a static picture. We also have information about what chemicals are in the sample. That means we know what is happening in there, but not what is doing it. That is a dynamic image. And now, I am trying to combine the static image with the dynamic image to get information about what bacteria are present in the intestine and also what they do there and how they interact," explained Smatana, who studied bioinformatics at FIT BUT and, during his Master's studies, he focused on finding and analysing enzymes with potential applications in industry.
Stanislav Smatana, who also works in the Centre for Research of Toxic Compounds, in the Environment at Masaryk University in addition to his doctoral studies at BUT, also received the Brno PhD Talent Award for his research project through which he received support from the South Moravian Centre for International Mobility and the city of Brno.
Author: Kozubová Hana, Mgr.
Last modified: 2020-06-26T15:11:11