Brazilian firm specializes in genomics, diversifies markets and products

Genetic marker to identify yeast strains is already used by 30 ethanol plants in five states.

FAPESP Research for Innovation – The Genotyping Group in Botucatu, São Paulo State, Brazil, comprises two firms: Genotyping Diagnósticos Genéticos, which specializes in genetic testing, and Biotecnologia Pesquisa e Inovação (BPI), which provides high-tech genomics services to manufacturers, universities and research institutions. The holding company is an investee of the São Paulo State Innovation Fund (FIP) and also has an angel investor.

FIP’s lead partner is Desenvolve SP, the state government’s development agency. Other investors include the Brazilian Innovation Agency (FINEP), FAPESP, SEBRAE-SP, the Development Bank of Latin America (CAF) and Jive Investments.

The two firms that combine genomics and innovation originated in biologist Débora Colombi’s postdoctoral genetics research, completed in 2006. With support from FAPESP, she studied mitochondrial protein expression in Saccharomyces cerevisiae, the baker’s and brewer’s yeast. Genetic studies of this yeast (and its various strains) to extend knowledge of its role in the fermentation process have a direct impact on the production of bioethanol from sugarcane, in which it plays a key role. 

“When I finished my research, I was contacted by a sugar and ethanol manufacturer,” Colombi recalls. “I found that the sugar and ethanol production process would be more efficient if a different technology was used for genetic analysis of the yeast used in fermentation vats.” 

Instead of karyotyping to identify and analyze the yeast’s chromosome profile, she proposed microsatellite molecular markers, repeated short DNA sequences that can be used to identify individuals or species genetically. 

Colombi then set up a laboratory for this specific purpose, called Genotyping Laboratório de Biotecnologia, and in 2011 had a project approved by FAPESP’s Small Business Innovative Research (PIPE) program. With support from FAPESP, she developed molecular markers to differentiate yeast strains during the ethanol fermentation process. “The industry validated the microsatellite technology, which has indeed proved much faster and more efficient than karyotyping,” Colombi says. The solution’s success among sugar and ethanol manufacturers attracted the angel investor.

Market diversification

Genotyping Laboratório de Biotecnologia initially focused on the ethanol industry, which made survival difficult between sugarcane harvests. Mastering the molecular marker technology enabled the laboratory to seize the opportunity to enter the genetic testing market. “We use second-generation sequencing technology to offer genetic testing to the market,” Colombi says.

For a time, the firm divided its efforts between genetic testing for the general public and research and innovation for the ethanol industry, universities and research institutions.

The amount of work doubled without jeopardizing its research activities. In 2013, Colombi submitted a new project to PIPE to resolve bacterial contamination, another serious problem faced by ethanol plants. The aim was to identify the potentially harmful microorganisms present in the fermentation process.

The project entailed the use of metagenomics to identify bacteria and metatranscriptomics to analyze gene expression in the bacteria detected in samples. The idea was to offer manufacturers a quick solution kit for incidences of contamination during the fermentation process, which typically lasts six to eight hours.

The product was developed and named MetaID, but its response time was not  fast enough for the needs of ethanol plants. The project’s main legacy, according to Colombi, was mastery of the metagenomics tools to enable the firm to meet demand from universities and research institutions for technologies relating to transcriptomics, whole genome sequencing and variant discovery, among others. To date, this knowledge has helped BPI prospect new markets such as cosmetics, for example.

In 2015, when the firm received investment from FIP, the funding came with a recommendation to split its activities. “So we set up Genotyping as a holding company: Genotyping Diagnósticos Genéticos does all the work with humans, and BPI does research and development,” Colombi explains.

Genotyping Diagnósticos Genéticos currently has ten employees, of whom half have either a PhD, a master’s degree or a specialization diploma, while BPI has five, of whom two have a PhD. The two firms reported very similar revenue in 2016. “Genotyping Diagnósticos Genéticos looks set to forge ahead in 2017,” Colombi predicts.

The difference in performance in favor of Genotyping Diagnósticos Genéticos is due, she says, to the fact that since 2016 health insurance plans have agreed to pay for certain tests that use next-generation sequencing (NGS). “This gives our company an advantage,” she notes. On the other hand, BPI’s performance may have been weakened by the decrease in official funding for scientific research and in investment by the ethanol industry.

Despite these problems, BPI’s genetic marker for yeast (called LeveID after the Portuguese word levedura, meaning yeast) is already being used by 30 ethanol plants in São Paulo State, Goiás, Mato Grosso, Minas Gerais and Paraná. Colombi aims to expand this market.

The research is also advancing. “We continue to seek a solution to the question of bacterial contamination,” Colombi says. Again supported by FAPESP’s PIPE program, the firm is investigating the production of a bacterium identification kit with instant detection based on gold nanoparticles modified with specific antibodies for selective determination of key contaminants. “The ethanol plant will get its answer in 20 minutes,” she promises.

Genotyping Diagnósticos Genéticos
http://genotyping.com.br
Contact: [e-mail]

BPI – Biotecnologia Pesquisa e Inovação
http://bpibiotecnologia.com.br/
Contact: [e-mail]