A group of researchers from the Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), an organization supervised by the Brazilian Ministry of Science, Technology and Innovations (MCTI), has published in the journal Nature Communications a study that explores some of the most modern resources of current science to reveal unprecedented and valuable details of the capybara’s digestive process.

The capybara, the largest rodent on the planet, is known for its ability to degrade very efficiently the biomass it consumes, but the details of the animal’s microbiota metabolism that contribute to this characteristic have not yet been elucidated. Researcher Mario Murakami recalls that, in Brazil, this animal is used to eating sugarcane. “Since Brazilian biodiversity is an invaluable source of biotechnological solutions, our hypothesis was that the microorganisms inhabiting capybaras’ intestines have, throughout evolution, developed highly effective molecular strategies for the degradation and use of this biomass of great industrial and economic importance. And that was demonstrated in our study.”

“Population and molecular inventory” of the gut microbiome

The meticulous and unprecedented work started with a complete survey of the bacteria present in the capybara’s intestine, in addition to the expressed genes and metabolites produced from plant fibers. To understand the processes of depolymerization of lignocellulosic fibers and the efficient transformation of sugars into energy, a vast combination of techniques, methodologies and resources, including synchrotron light at the MX2 and SAXS1 beamlines of the Brazilian Synchrotron Light Laboratory (LNLS), was required, from the population scale of microorganisms to the atomic and molecular level of enzymes.

Discovery

The elucidation of the entire digestive process of the capybara, by mapping the main metabolic pathways and exploring what is called “genomic dark matter”, revealed new microorganisms and two new families of enzymes, with potential use in biotechnological applications.

One of the new protein families, named CBM89, is related to the recognition of carbohydrates abundant in grasses such as sugarcane. The second new family of proteins, named GH173, showed promise for applications in the food.

“The first family proteins have the potential to be tested in enzymatic cocktails used in industrial processes for the manufacture of biofuels, biochemicals and biomaterials. Those from the second family can be tested in processes of metabolizing milk derivatives, to break down lactose, for example”, explains researcher Gabriela Persinoti.

According to researcher Mariana Morais, the novelty of the work leaves another important legacy for the deepening of research on Brazilian biodiversity: “As the approach was successful, this entire methodology can be useful for studying microbiomes from other sources of Brazilian biodiversity in depth.”

Next steps

As these are new families of proteins, the next steps are related to the expansion of knowledge about the functions and activities of each one of them.

In order to better assess the biotechnological potential, the next stage of the research foresees the use of Sirius’ research stations, the latest generation synchrotron light source designed and operated by CNPEM, in addition to the application of knowledge in the areas of synthetic biology and bioinformatics.

Source: Cabral, L., Persinoti, G.F., Paixão, D.A.A. et al. Gut microbiome of the largest living rodent harbors unprecedented enzymatic systems to degrade plant polysaccharides. Nat Commun 13, 629 (2022). DOI: 10.1038/s41467-022-28310-y