Student Develops Innovative Method for Detecting Oil Using PCR Tests
Fedor Shirshikov, a student of the Master's in Corporate Research, Development and Innovation Management at HSE University, has proposed an innovative technology for identifying oil and gas fields by detecting indicator microbes using PCR tests. The new method could help reduce the number of costly dry drilling operations. With this project, the student made it to the finals of the GreenTech Sustainable Development technology accelerator organised by the Skolkovo Foundation. In this interview, he explains why a biologist decided to study innovation management and how the oil industry inspired his startup idea.
— How did you choose the topic for this project?
— My first degree was in microbiology from Kazan Federal University. After that, I worked in Moscow and St Petersburg at the intersection of microbiology, molecular biology, and bioinformatics. Following my doctoral studies in molecular biology at the Institute of Bioorganic Chemistry of the Russian Academy of Sciences and my first experience in a commercial laboratory detecting microbes dangerous to potatoes, I realised that I was drawn to project-based work. However, I lacked the skills needed to manage the research and development process, so I decided to enrol in the relevant educational programme at HSE University.
The project, which I chose as the topic of my term paper, focuses on the development and commercialisation of a more accurate technology for identifying oil and gas deposits using indicator microbes. The startup idea emerged from my ten years of experience and my PhD research on developing diagnostic tests based on PCR (polymerase chain reaction), a method that became widely known during the COVID-19 pandemic. My work aims to create a new commercial service, the economic impact of which will be assessed as part of the research. The economic component of the project is supervised by Anna Solodikhina, Senior Lecturer at the HSE School of Innovation and Entrepreneurship, while I am personally responsible for the biological aspect.
I once heard a quote from Academician Yuri Ovchinnikov that became my personal source of motivation: 'We need to take on work that today seems completely unrealistic and impossible. In a year, it will be exactly the right thing.' That is why I decided to immerse myself once again in a completely new field—petroleum microbiology and geological exploration—where I am still an absolute beginner.
I was once a similar beginner in the field of PCR, having come from structural protein bioinformatics and not even knowing how to pipette reagents into test tubes. Some of the basics were shown to me by colleagues, while the rest I had to learn from scientific papers as I gradually acquired hands-on wet-lab skills. My experience at the Institute of Bioorganic Chemistry of the Russian Academy of Sciences has, in my view, shaped a certain research style that I try to carry into every new project I take on. I find it difficult to describe, but it usually feels intuitive.
— What is the target audience of your startup?
— The project has been named OASYS (Oil Assessment Systems). In Russia, hydrocarbon deposits act as 'oases' for certain microbial communities. As a new tool for detecting such indicator microbes, we propose creating rapid PCR-based tests. A preliminary list of promising genomic targets in indicator microbes has already been compiled and will be further expanded using MorphoCatcher, a tool we have developed. The concept of this new approach to oil exploration is relatively simple, and both its principles and methods of implementation are currently being prepared for patenting.
Our target audience includes the exploration departments of oil and gas production companies as well as oilfield service companies. Russia has now entered the era of 'green seismics,' when geophysical exploration is conducted in a fast and environmentally friendly manner, without extensive deforestation. In Siberian forests, clearings or grid-like patterns are visible from above; these existing corridors can potentially be used in new ways. However, the method is applicable not only on land but also offshore.
Until now, the most accurate way to determine the presence of oil in the subsurface has been through drilling a well, where a gush of oil is the clearest sign of successful exploration.
The problem is, first, that drilling wells is extremely expensive, especially in the Arctic and offshore environments, while drilling efficiency is very low. Approximately 88% of wells turn out to be dry, meaning no oil is found. Even in the most intensively explored regions, such as Western Siberia or Tatarstan, the minimum cost of exploratory drilling is about 1 billion roubles. Thus, the issue is clearly highly acute, even for oil companies with substantial financial resources. As existing deposits are being depleted, the problem is likely to become even more severe in the future.
Green seismic technology makes it possible to visualise the geological structure of the subsurface and identify cavities in which oil and gas typically accumulate. However, it does not allow us to determine which of these cavities actually contain hydrocarbons and which represent false indications of a deposit. To avoid drilling every potentially oil-bearing structure and to reduce exploration costs, there is a need for a relatively fast and inexpensive method for delineating the contours of hydrocarbon deposits on a terrain map.
About 100 years ago, geochemists observed that soils above oil and gas deposits are often saturated with low-molecular-weight hydrocarbons. For certain microbial species, methane, ethane, propane, and other light hydrocarbons serve as common nutrient substrates. By consuming hydrocarbons migrating from deep formations, these microbes can introduce significant errors into gas survey methods, a widely used approach for oil exploration in which volatile hydrocarbons are directly measured using gas chromatography and mass spectrometry. In addition, there are microbial groups that produce methane themselves, which can only be distinguished through isotopic analysis—an important factor that must also be taken into account.
Microbes, rocks, oil, and micro-seepages of gas form a single natural ecosystem, and it is misleading to study or analyse its components in isolation. The analysis of hydrocarbons, hydrocarbon-oxidising microbes, and seismic data should therefore be integrated and mutually reinforcing. No single method can be universal or provide a complete picture on its own. However, when different approaches are applied to the same problem in combination, they can produce a synergistic effect.
Soviet geochemist Grigory Mogilevsky was the first to propose detecting such microbes by cultivating them in the laboratory and using the resulting data to construct predictive geological maps. This approach helped refine the boundaries of oil deposits and provided more accurate estimates of hydrocarbon potential than the gas survey method. However, a second problem arises: not all microbes can be cultivated in the laboratory. Many species are unculturable and require a natural microbial community to grow.
My goal is to improve the accuracy of Mogilevsky’s microbiological method by using PCR-based molecular tests to detect indicator microbes among hundreds of thousands of other microbial species. This is a particularly challenging problem. Ultimately, however, it could significantly reduce the cost of drilling wells, and its economic effect can be estimated as the cost savings from avoiding dry wells.
— How did the accelerator finals go?
— The projects were evaluated by senior representatives of the Tatneft Centre for Technological Development and its subsidiary TN-Biotech. The opportunity to present in front of the leadership of one of the industry’s major players is extremely valuable in itself. For me in particular, it was especially significant, as I was the only student among the participants who had founded a startup without establishing a legal entity. I would also like to thank the experts of the Skolkovo Foundation for their attention to the substance of my application and the progress of the project.
The main purpose of my participation was to test the demand for the proposed approach of using PCR to detect microbial indicators of oil. When I applied to the accelerator, I was fully confident in my skills as a test developer: in both bioinformatics and wet molecular biology, I had already developed solutions applicable across various areas of biotechnology. At the same time, I realised that a fully functional test system would only emerge with the involvement of a relevant industry partner.
— What are the prospects for the project's further progress?
— Many people are familiar with PCR, how it works, and how diagnostic tests are developed. However, the field of diagnostics involves many pitfalls. Searching for indicator microbes in soil can be compared to finding a needle in a haystack.
For now, I can and will continue pursuing the project on my own. From a theoretical perspective, this is possible within the scope of my self-selected term paper at HSE University. On the practical side, I plan to improve the software for the identification of new target genes in microbial genomes. There is still a great deal of work ahead. The project is new and promising, and I am full of enthusiasm.
During the pandemic, virtually everyone heard about PCR tests and many even took them. However, the idea of using PCR for oil exploration initially occurred to only one person—or perhaps to several individuals independently. After the accelerator finals, many more people became aware of this concept. Thus, the idea has now spread, but only its originator holds the potential solution for its implementation. The life of ideas is a remarkable phenomenon.
Sometimes the first company to bring a product to market fails, discouraging customers and stalling the development of the market itself. In such cases, the second or even third entrant may succeed—but only if they learn from the mistakes of their predecessors.
This is what we are taught in the master’s programme at HSE University. I am glad to be able to experience firsthand what I have heard from my teachers about ideas, innovation, and startups—their dizzying successes as well as their equally notable failures. Interestingly, learning from mistakes can be even more valuable, as they teach us and shape our experience. Therefore, we must keep trying.
I hope I will have enough energy and ideas to contribute to various industries and participate in other accelerators. I would therefore like to express my gratitude to my academic supervisor, Anna Solodikhina, for believing in this project and discussing ideas with me; to Dmitry Ognev for his inspiring lectures on invention; and to Natalya Polyakova for the invaluable advice she provided during the intellectual property management course.
The accelerator helped me refine the project for the oil and gas industry, and I am also grateful to my tracker and to all organisers of the Skolkovo Foundation event.
However, HSE University has been the best accelerator for me
The concentrated expertise and experience of its lecturers in the field of entrepreneurship, shared with students, is truly energising, and this momentum makes one feel unstoppable.
— Do you believe you will be able to build on your experience of participating in the accelerator in your future communication with investors or customers?
— I am confident that becoming a finalist of the Skolkovo Foundation accelerator will be an advantage for me. My presentation is now finalised, and my pitch has been carefully refined to ensure it is clear and accessible to the target audience. Hundreds of applications were submitted to the programme, and only a few dozen projects reached the finals. This suggests that my project aligns with real business needs. For anyone familiar with the Skolkovo accelerator process, this achievement serves as a mark of quality.
