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Bioinformatics specialists reveal the secret of antibiotic-resistant bacteria

Researchers from the Scientific Research Institute of Physical-Chemical Medicine, MIPT, the company M&S Decisions and the research department of Yandex have built a computer model of the interaction between different bacteria, and between bacteria and the gut wall. This has led them to explain how antibiotic-resistant microbes develop and spread; details of the study have been published in the journal PLOS One.

The human intestine contains trillions of different bacteria, which together are called the microbiome. Bacteria protect us from harmful microorganisms, produce digestive enzymes, and help the immune system to function normally. Many diseases, such as obesity, Crohn’s disease, colon cancer, and other inflammatory processes are associated with a change in the gut microbiome. The researchers built a model of the interaction between two types of bacteria and the intestine and they determined what happens when antibiotics are taken that kill a large number of microorganisms.

“In biomedical science, we are now actively gathering information that is extremely important for bioinformatics – information which is enabling us to build models of complex systems. In our study, we used a simple modelling method – Agent Based Modelling (ABM) – to recreate the processes involving bacteria that take place in the gut and explain some interesting effects when resistivity occurs,” said Dmitry Alexeev, Deputy Head of MIPT’s Laboratory of Systems Biology and the corresponding author of the study.

The researchers were interested in a number of important issues – firstly, the speed at which the number of bacteria was restored after antibiotic therapy. Secondly, the scientists were interested in finding what proportion of bacteria was not affected by antibiotics, and thirdly the model described in detail the process of feedback between bacteria and the intestinal wall. The intestinal wall actively absorbs certain substances and produces others, which affects the number of bacteria and their “state of health”: if the numbers of bacteria in these processes are altered, it is difficult to obtain proper results.

The substances produced by bacteria and the intestinal walls were one of the main focal points in the new model. These compounds, which are formed by the bacterial fermentation of carbohydrates, may perform different functions at once: e.g. they can be toxins for one type of bacteria, and “food” for another type. If certain bacteria begin to produce too much of a substance that is poisonous to them, their numbers automatically decrease – scientists call this negative feedback. The intestinal wall can also produce either compounds that are harmful to bacteria (but not to the intestines themselves!), or carbohydrates that microorganisms can digest as nutrients.