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  • Adaptive Laboratory Evolution (ALE) for stress tolerance in Saccharomyces cerevisiae and other microorganisms, uncovering genetic bases of robustness for industrial environments.                            

  • Genome sequencing & bioinformatics to assemble genomes, map variants, interpret multi-omics data, and guide data-driven strain improvement.                                                                                        

  • Genome engineering with the EasyGuide CRISPR suite and in vivo multipart DNA assembly, enabling precise, rapid, and scalable editing of microbial genomes.                                                              

  • Design of microbial cell factories for bio-based products, translating synthetic biology and evolution into sustainable bioprocesses and next-generation biorefineries.

We apply genomics and experimental evolution to Saccharomyces cerevisiae, Escherichia coli, and other microbes to uncover the genetic changes that drive adaptation to industrial stresses. Using the EasyGuide CRISPR toolkit and in vivo multipart DNA assembly, we perform precise, rapid genome edits to test genotype–phenotype relationships. Our aim is to understand evolution at the molecular level and to build robust microbial cell factories for sustainable, bio-based products. Our lab is located in Rio Claro at the Bioenergy Research Institute (IPBEN) of São Paulo State University (UNESP).

Current Projects

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ALE for yeast tolerance to lignocellulosic hydrolysates

(Saccharomyces cerevisiae)



New advances in adaptive evolution protocols, QTL mapping, and CRISPR/Cas9 technologies are proposed to enhance yeast tolerance to lignocellulosic hydrolysates. Learn more...

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EasyGuide CRISPR 

(S. cerevisiae and E. coli)

Leveraging in vivo cloning in yeast and E. coli to assemble gRNA and donor cassettes for multilocus edits, CRISPRi, CRISPRa, and base editors. EasyAssembler: rapid in vivo assembly of multipart DNA.

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Adaptive evolution of Escherichia coli for  sucrose consumption under anaerobic conditions

Yes, we also conduct evolutionary experiments with E. coli, which we intend to use as a workhorse for the production of polyhydroxyalkanoates from sugarcane 

sucrose. Learn more...

Experimental evolution of ethanol tolerance

(Saccharomyces cerevisiae PE-2)



Here we use the S. cerevisiae strain PE-2, widely used in the Brazilian bioethanol industry, to challenge cellular adaptation to an increasing ethanol concentration. Learn more...

November 2023 - CNPq Universal project granted to our Lab to support the CRISPR EasyGuide project!   

October 2023 - Lucas de Bem has been granted with a sandwich  PhD  scholarship from FAPESP. He will apply the ReMaSSing to the synthetic Sc2.0 yeast genome at the Cai Lab, UK! Congrats Lucas!   

September 2023 - We welcome MSc. Sara Franchin and MSc. Dione Jordan as new members of our team!

 

August 2023 - We approved a new FAPESP grant to expand our EasyGuide system!

April 2023 - Dr Ana P Jacobus joined the Institute SENAI for Innovation in Biotechnology, São Paulo. A great opportunity to branch out our work! Good luck Ana! 

 

April 2023 - Yasmine defended her PhD qualification with merits! Congrats Yasmine!

Feb 2023 - FAPESP/SPRINT project awarded to Dr. Ana P Jacobus to start a collaboration of our lab with Prof. Bastian Blombach from TUM Straubing. Congrats Ana!

Out 2022 - The EasyGuide CRISPR paper is out! 

Out 2022 - Best poster prize for Jef Gross at the EMBO workshop.

See the poster!

 

Out 2022 - Best poster prize for Yasmine Alves Menegon at the conference Key Technologies in the Bioeconomy. 

July 2022 - Yasmine A. Menegon has been granted with a CAPES PhD  sandwich scholarship to Australia! Congrats!

April 2022 - Our paper on yeast adaptive laboratory evolution to lignocellulosic hydrolysates is out!

April 2022 - Lucas Souza de Bem granted with a FAPESP PhD scholarship. Congrats Lucas!

January 2022 - Book chapter on hemicellulosic biorefineries.

July 2021 - Our new paper on commercial bioethanol yeasts has been published! 

April 2021 - Our paper on bioethanol yeasts genomics in now out!

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Genome Engineering and Evolution of Microorganisms

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