It Takes Guts: Novel Enzymes From the Capybara Microbiome Could Help Transform Plant Material Into Biofuels

By Vilhelmiina Haavisto and Allison Hung

In recent years, the capybara has been launched into internet stardom as the world’s largest and chillest rodent. This giant rodent looms over its guinea pig relatives by nearly a meter, and has endeared millions of viewers by forming friendships with all animals alike. Yet, what’s most interesting about the capybara may be what is going on under the hood. The gut microbiota of herbivores such as the capybara harbor sophisticated systems to degrade complex plant fibers that are a hallmark of the herbivore diet, producing energy for both the host and themselves. 

Until now, the capybara gut microbiota was mostly a ‘black box’ in terms of its microbial community and how they break down their host’s diet, which includes complex, difficult-to-degrade fibers common to aquatic plants such as lignocellulose and pectin. A group of researchers from the Brazilian Biorenewables National Laboratory (LNBR) in São Paulo recently published their findings from a deep-dive into the capybara gut, in an effort to develop biotechnological solutions for sustainable development. 

Why the capybara?

The motivation for studying the capybara stems from the ability of wild populations in southeastern Brazil, which the researchers sampled, to incorporate large amounts of sugarcane into their diet. Sugarcane has great potential as a raw material for producing biofuels, and finding efficient ways to degrade it is crucial for developing sustainable, high-yield biofuel production. Citing the value of Brazilian biodiversity as a source of biotechnological solutions, LNBR Scientific Director and last author of the study Dr Mario Murakami explained that they believed the capybara gut would contain microbes with highly effective strategies for degrading complex plant fibers. 

No stone was left unturned as the researchers used an arsenal of molecular techniques to characterize the capybara gut’s diversity in both form and function. Altogether, this integrated approach led to great insight into the wondrous world of the capybara gut, including the discovery of two novel enzyme families and several species or genera of microorganisms harboring large enzyme clusters of biotechnological interest.

Breaking down tough plant fibers with CAZymes

These two enzyme families fall into what are categorized as carbohydrate active enzymes, or CAZymes: enzymes that degrade and modify a multitude of carbohydrates including complex plant fibers. Unsurprisingly, the gut microbiota of herbivores including the capybara are ripe for CAZyme discovery.

CAZymes for degrading complex plant fibers like cellulose and lignin are a common feature of microbes inhabiting the guts of herbivores such as cows and elephants, who ingest large amounts of plant fibers every day. While the human genome only encodes 17 CAZymes, the human gut microbiota collectively encodes hundreds, and those of herbivores such as camels and buffaloes encode even more still. These microbes help their herbivorous hosts glean energy and nutrients from these tough fibers, as well as produce vitamins and detoxify compounds that plants use to defend themselves. 

Learning how microbes in the gut get the job done can help us to apply these strategies to efficiently convert plant fibers into value-added products like biofuels. Finding enzymes and chemical pathways that can break down complex fibers is critical to maximize the yield of this bioconversion process. 

Towards a larger enzymatic toolbox

Starting from fresh intestinal samples, the researchers were able to isolate millions of DNA sequences, which they stitched together using bioinformatic tools into putative whole genomes. These advanced metagenomic techniques showcase a new age for enzyme discovery, as scientists are beginning to directly examine microbes in their native contexts, allowing them to uncover rare enzymes that would have been missed in traditional studies. Using metagenomics, the researchers uncovered several new, large CAZyme clusters that would not have been identified otherwise.

One family of CAZymes that the researchers discovered has an unusual structure that is involved in recognizing a specific type of plant fiber called xylan. The researchers speculate that the unconventional structure could be useful for designing and engineering different kinds of enzymes, increasing the variety of enzymatic tools for transforming complex carbohydrates. 

Another major discovery from the metagenomic analysis came from a Bacteroidetes species harboring a large set of CAZymes. Examination of these enzymes, specifically a GH-A β-galactosidase, led to the discovery of an entirely new CAZyme family. By examining neighboring CAZymes, the researchers were able to deduce that it digests pectins, highly complex polysaccharides that are frequently found in plant cells. 

β-galactosidases are already broadly employed in the food and beverage industry, where they are used to produce lactose-free dairy products and the transformation of whey into a multitude of food products. Meanwhile, pectins are considered valuable biomass for biofuel production as they are abundant in plant-based food waste, which could be upcycled to produce biofuels. As such, the discovery of this new family could help to expand our enzymatic toolbox for biomanufacturing using complex plant fibers. 

Enzymes most wanted

The enzymes discovered in the capybara gut are just some among many discovered from other unexpected places. For example, wax moth larvae and superworms are able to feed on polyethylene, one of the hundreds of largely single-use plastics we produce. This appears to be thanks at least in part to their gut microbes, which produce enzymes that break carbon bonds found in both plastic and the host’s normal diet. Indeed, so-called ‘plastic-eating worms’ are rapidly becoming a trendy branch of research into enzymatic plastic degradation.

Like many understudied microbial habitats, the capybara gut presents a treasure trove of discoveries. Thanks to the variety of techniques they used, the researchers were able to characterize this diversity in microbial life and function from many angles, from the taxonomic composition of the community to the activities and structures of their enzymes. Most importantly for the group’s broader research goals, their work resulted in the discovery and detailed characterization of key enzymes that could help us work our way to a more sustainable future.

Vilhelmiina Haavisto is a Microbiology and Immunology MSc stu­dent at ETH Zürich in Switzerland, where she works with freshwater microbial communities.

 

 

 

Allison Hung is a PhD student in Molecular & Cell Biology at the University of California, Berkeley, where she investigates gut microbial colonization.

 

 

 

Featured image source.