Herbivores have specialized gut microbiota to digest complex carbohydrates found in plants. We have been investigating the gut microbiota of wild capybara, the largest living rodent dwelling wetlands in South America, which led to the discovery of novel microorganisms and enzymes dedicated to breaking down distinct types of carbohydrates found in its diet and of biotechnological relevance ^1,2.

In the current work published on npj Biofilms and Microbiomes, by exploring the enzymatic systems from the capybara gut microbiota, we revealed that a gene cluster (known as Polysaccharide Utilization Locus (PUL)) featuring the same gene composition in herbivores compared to humans exhibits a function expansion covering different types of non-cellulosic β-glucans. This gain of function highlights how the metabolic functions of gut microbiota from herbivores can be shaped by their feeding habit.

The challenges of β-glucans depolymerization and comparison of human and herbivore digestion systems

Non-cellulosic β-glucans, abundant in plant cell walls, algae, and fungi, pose a challenge for digestion and require specialized enzymes found in gut microbiota. In the human gut, bacteria like Bacteroides sp. efficiently digest mixed-linkage β-glucans ³, but herbivores’ microbiota must handle additional polysaccharide variants due to exclusive and complex plant-based diets.

The work performed by Mandelli, Martins, Chinaglia et al. identified and characterized a PUL from Alloprevotella sp. MAG60, a novel bacterium from Bacteroidota phylum found in the capybara gut. This PUL shares genetic similarities with Bacteroides ovatus PUL from the human gut, including essential enzymes, like endo-β-glucanase from the GH16_3 family and β-glucosidases from the GH3 family, which degrade linear mixed-linkage β-glucans. However, the PUL from the herbivore gut exhibits expanded functionality, enabling it to also degrade substituted β-glucans containing β(1,6) linkages, a capability that relies on the activity of the CapGH3a enzyme, a β-glucosidase active on β(1,6) linkages (Figure 1). This evolutionary adaptation enables herbivores to process a broader spectrum of plant polysaccharides, highlighting the microbiota adaptation to tackle the dietary demands of these animals.

Mechanistic adaptations in β-glucosidases: a specialist enzyme widespread in the microbiota of herbivores

The endo-β-glucanase (CapGH16_3) and β-glucosidase (CapGH3b) from the herbivore gut Bacteroidota exhibit structural and functional similarities to the enzymes in B. ovatus PUL, dictating similar roles on linear mixed-linkage β-glucans degradation. However, another β-glucosidase, CapGH3a, diverges significantly, with its structure adapted for recognizing β(1,6)-glycosyl units. This unique capability arises from the presence of only one aromatic platform in the product release area, a tryptophan residue that provides a necessary degree of freedom for the binding and stabilization of β(1,6)-glucosyl units (Figure 2). The aforementioned tryptophan belongs to a conserved loop observed only in β(1,6)-glycosidases of the GH3 family.

Similar PULs containing orthologs of CapGH16_3, CapGH3b, and CapGH3a have been identified in the microbiota of other herbivores, including goat, buffalo, sheep, yak, and deer. It indicates a common biochemical strategy to efficiently degrade β(1,6)-substituted glucans in herbivore microbiota. This contrasts with the human microbiota, reflecting dietary and evolutionary differences across species.

Biological and biotechnological implications

The expanded capabilities of the herbivore gut PUL reflect the unique evolutionary pressures faced by these animals and their gut microbiota. With access to a broader range of dietary plant carbohydrates, these animals need a microbiota with metabolic functions capable of breaking down complex carbohydrates efficiently. The ability to digest substituted β-glucans not only enhances nutrient absorption but also ensures optimal energy extraction from varied plants. These findings open new opportunities for biotechnological applications including bioenergy and animal nutrition by facilitating the conversion of plant biomass into fermentable sugars either for industrial applications or host carbon uptake.

Concluding remarks

This finding modifies our current understanding of microbiota evolution and functional adaptability by demonstrating that even genetically similar systems, like PULs in humans and herbivores, can diverge functionally to meet environmental and dietary demands. For herbivores, the ability to efficiently degrade complex β-glucans is essential for survival and reflects a well-tuned symbiotic relationship with their gut bacteria.

References:

1. Cabral, L. et al. Gut microbiome of the largest living rodent harbors unprecedented enzymatic systems to degrade plant polysaccharides. Nat Commun 13, (2022).
2. Martins, M. P. et al. Glycoside hydrolase subfamily GH5_57 features a highly redesigned catalytic interface to process complex hetero-β-mannans. Acta Crystallogr D Struct Biol 78, 1358–1372 (2022).
3. Tamura, K. et al. Molecular Mechanism by which Prominent Human Gut Bacteroidetes Utilize Mixed-Linkage Beta-Glucans, Major Health-Promoting Cereal Polysaccharides. Cell Rep 21, 417–430 (2017).