Platform identifies soil microorganisms that cause disease

By Roseli Andrion  |  FAPESP Innovative R&D – One of the main challenges of precision agriculture is mapping the community of microorganisms in the soil, both beneficial and pathogenic. Biologist Rafael Silva Rocha founded the biotech startup ByMyCell in Ribeirão Preto (São Paulo state, Brazil) to facilitate this process.

The firm’s researchers use next-generation DNA sequencing to identify soil microbiota with a high degree of accuracy and more affordably than the alternatives available in the marketplace. They can detect pathogens and help farmers make decisions that boost yields and reduce the use of agrochemicals.

“We supply facilitated genomics via a robust cloud-based data analysis platform to help clients speed up research and development,” Silva Rocha said. The firm currently focuses on agricultural solutions. It initially targeted companies and research groups, building a client portfolio that includes the University of São Paulo (USP), the State University of Campinas (UNICAMP), São Paulo State University (UNESP), federal universities, the Brazilian Agricultural Research Corporation (EMBRAPA) and Butantan Institute. Altogether, it has more than 200 clients.

ByMyCell’s founders decided to pivot to agriculture in light of the difficulty of identifying pathogenic microorganisms on farms. “We made some changes to the platform and started offering the solution to farmers. It was a necessity that arose during the process,” Silva Rocha said.

The platform was enhanced via a project supported by FAPESP’s Innovative Research in Small Business Program (PIPE). It can identify any microorganism. More than 300,000 can be mapped in a single analysis. “Best of all, it’s affordable,” he said.

The methodology has been used to identify pathogenic fungi, the main cause of crop disease. The model is unique, and no one else offers the same service in Brazil. Most of ByMyCell’s competitors supply raw data. “This has enabled us to grow quickly. Some players have imported solutions, but the cost is high and precision low, as they’re not designed for use in Brazil,” he said.

ByMyCell’s platform calculates the risk of disease on a farm and compares the result with its exclusive database to make predictions. “These are provided in a spreadsheet or directly on a map of the farm, which is user-friendly because the agronomist sees exactly where each microorganism could be active,” he said.

The firm also suggests bioinputs produced in Brazil to treat each disease. Imported agrochemicals currently account for 50% of production costs on average. “Farmers want to reduce this expense. Our mapping lets them target diseases precisely because it identifies all the microorganisms. Moreover, they can opt for local products, which are more sustainable,” Silva Rocha said.

Crop losses due to fungal disease average 23% worldwide. The platform could lead to a reduction in these losses in the medium to long term insofar as it enables farmers to combat disease correctly. “They can control microorganisms and diseases they didn’t even know were there,” he said.

The price of the analysis corresponds to between 0.3% and 0.5% of production costs, according to Silva Rocha. “It’s very inexpensive, especially compared to the cost of agrochemicals, which account for about 50%,” he said.

Partnerships with universities

Silva Rocha has extensive experience in the segment. After graduating in biology from the Federal University of Pará (UFPA), he earned a PhD in molecular biology at the Autonomous University of Madrid (Spain), where he specialized in bioinformatics. Later he held postdoctoral fellowships at Madrid’s National Center for Biotechnology (CNB-CSIC), where he worked on systems and synthetic biology, and at the University of São Paulo’s Ribeirão Preto Medical School (FMRP-USP), working on systems biology. He also served as a university professor in FMRP-USP’s Department of Cellular and Molecular Biology.

In 2022, he decided to devote all his time to setting up and running ByMyCell. He applied his expertise in genomic data analysis to development of the solution. “I identified demand for the product while I was still working at the university,” he said.

The startup continues to partner with academia. “We have three ongoing projects. The firm’s agility isn’t possible for universities, but they have advantages we lack. The partnerships help train and develop professionals, while also offering the possibility of bringing in talented people to work for the firm,” he said.

According to Silva Rocha, few universities conduct genomics research entirely in the cloud. “Until recently, they were still buying physical servers, so many students have no experience with the cloud. Our partnership with USP has been fruitful, lending us undergraduates in their last year as interns. We train them to use the technology and prepare them for the labor market. Two out of five interns have been hired as team members so far,” he said.

The startup has two founding partners and ten staffers. The team doubled in size in the last two months thanks to the projected supported by PIPE-FAPESP. “ByMyCell has sufficient revenue to pay its own bills, so we were able to use the funding from PIPE to create a research and development group,” he said. More specialists will be hired by the end of the year, taking the workforce to 15 people.

FAPESP’s support via PIPE was fundamental to help the firm expand, which it did differently from most startups supported by the program. “We used our own capital to set up the firm, but an angel investor later came on board and enabled us to develop faster,” he said. The learning curve accelerated further thanks to input from clients, and the firm was able to bid for funding from PIPE in early 2023.

Applications in human health

The technology developed by the firm’s researchers can also be used in the human health segment. For example, it can sequence viral DNA, as was necessary during the COVID-19 pandemic, when the characteristics of the novel coronavirus had to be understood as part of the effort to combat the disease.

The startup has plans for this niche. “Many human pathogens are poorly understood, and there are cases of infections that aren’t treated adequately owing to inaccurate or imprecise diagnosis. A good example is Sporothrix, a fungus often confused with Leishmania, a protozoan parasite. Imagine having a test that could examine all microorganisms instead of analyzing them one by one,” he said.

The health sector is more highly regulated so that adaptations will be required. “To win certification for our lab in this sector, we would have to invest at least USD 20,000 for starters,” he said. The firm is studying the possibility and is ambitiously aiming at offering this kind of solution to the market in three to five years.

“In the next three years, we’ll continue to focus on agriculture, where demand is still attractively high. We’ll then have achieved technological and entrepreneurial maturity to move into human health.”